I am trying to understand what sample it is correct to use when estimating the models using the control function (CF) approach. Below, I explain what I mean.

The CF approach is an alternative to xtivreg, fe estimation. Suppose X is an endogenous independent variable. In the CF approach, we first run
xtreg X Z C1 C2, fe, where
C1 and C2 are controls from the first stage and Z is an instrument); then predict residuals with
predict CF, resid
and then insert CF in the first stage:
xtreg Y X C1 C2 CF, fe
In this case, coefficients for X, C1, and C2 should be the same in both xtreg Y X C1 C2 CF, fe and xtivreg Y C1 C2 (X = Z), fe, while standard errors will differ if we do not adjust the ones from xtreg, fe via bootsrapping (I did not use bootstrapping in order not to create additional confusion).

Indeed, here are the results of xtreg, fe and xtivreg, fe I derived using the nlswork data:

xtreg, fe (errors not bootstrapped)
Code:
webuse nlswork, clear
quietly xtreg tenure union south age c.age#c.age not_smsa, fe
predict cf, resid
xtreg ln_w tenure age c.age#c.age not_smsa cf, fe

Fixed-effects (within) regression               Number of obs     =     19,007
Group variable: idcode                          Number of groups  =      4,134

R-sq:                                           Obs per group:
     within  = 0.1328                                         min =          1
     between = 0.2365                                         avg =        4.6
     overall = 0.2073                                         max =         12

                                                F(5,14868)        =     455.53
corr(u_i, Xb)  = 0.2033                         Prob > F          =     0.0000

------------------------------------------------------------------------------
     ln_wage |      Coef.   Std. Err.      t    P>|t|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
      tenure |   .2403531   .0151385    15.88   0.000     .2106797    .2700264
         age |   .0118437   .0036499     3.24   0.001     .0046894     .018998
             |
 c.age#c.age |  -.0012145   .0000798   -15.22   0.000    -.0013709    -.001058
             |
    not_smsa |  -.0167178   .0137527    -1.22   0.224    -.0436748    .0102393
          cf |  -.2227325   .0151602   -14.69   0.000    -.2524484   -.1930167
       _cons |   1.678287   .0659452    25.45   0.000     1.549027    1.807548
-------------+----------------------------------------------------------------
     sigma_u |  .38999138
     sigma_e |  .25552281
         rho |  .69964877   (fraction of variance due to u_i)
------------------------------------------------------------------------------
F test that all u_i=0: F(4133, 14868) = 8.30                 Prob > F = 0.0000
xtivreg, fe:
Code:
xtivreg ln_w age c.age#c.age not_smsa (tenure = union south), fe

Fixed-effects (within) IV regression            Number of obs     =     19,007
Group variable: idcode                          Number of groups  =      4,134

R-sq:                                           Obs per group:
     within  =      .                                         min =          1
     between = 0.1304                                         avg =        4.6
     overall = 0.0897                                         max =         12

                                                Wald chi2(4)      =  147926.58
corr(u_i, Xb)  = -0.6843                        Prob > chi2       =     0.0000

------------------------------------------------------------------------------
     ln_wage |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
      tenure |   .2403531   .0373419     6.44   0.000     .1671643    .3135419
         age |   .0118437   .0090032     1.32   0.188    -.0058023    .0294897
             |
 c.age#c.age |  -.0012145   .0001968    -6.17   0.000    -.0016003   -.0008286
             |
    not_smsa |  -.0167178   .0339236    -0.49   0.622    -.0832069    .0497713
       _cons |   1.678287   .1626657    10.32   0.000     1.359468    1.997106
-------------+----------------------------------------------------------------
     sigma_u |  .70661941
     sigma_e |  .63029359
         rho |  .55690561   (fraction of variance due to u_i)
------------------------------------------------------------------------------
F  test that all u_i=0:     F(4133,14869) =     1.44      Prob > F    = 0.0000
------------------------------------------------------------------------------
Instrumented:   tenure
Instruments:    age c.age#c.age not_smsa union south
------------------------------------------------------------------------------
As you could see, coefficients are the same, just standard errors differ (standard errors equalize once bootstrapped that confirms that both approaches yield the exact same results when the same instrument is used).

However, my question is about which sample in the first stage it is correct to use once our explanatory variables are lagged?

Fixed-effects IV estimator:
Code:
xtivreg ln_w l.age cl.age#cl.age l.not_smsa (l.tenure = l.union l.south), fe

Fixed-effects (within) IV regression            Number of obs     =      7,500
Group variable: idcode                          Number of groups  =      3,294

R-sq:                                           Obs per group:
     within  =      .                                         min =          1
     between = 0.0685                                         avg =        2.3
     overall = 0.0571                                         max =          6

                                                Wald chi2(4)      =   80781.56
corr(u_i, Xb)  = -0.5474                        Prob > chi2       =     0.0000

------------------------------------------------------------------------------
     ln_wage |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
      tenure |
         L1. |   .1755435   .0389611     4.51   0.000     .0991811    .2519059
             |
         age |
         L1. |   .0106753   .0134104     0.80   0.426    -.0156085    .0369592
             |
      cL.age#|
      cL.age |  -.0008867   .0002305    -3.85   0.000    -.0013384   -.0004351
             |
    not_smsa |
         L1. |  -.0452809   .0509685    -0.89   0.374    -.1451773    .0546154
             |
       _cons |   1.671945   .2302329     7.26   0.000     1.220697    2.123194
-------------+----------------------------------------------------------------
     sigma_u |  .59050356
     sigma_e |  .54146412
         rho |  .54324114   (fraction of variance due to u_i)
------------------------------------------------------------------------------
F  test that all u_i=0:     F(3293,4202) =     1.08       Prob > F    = 0.0089
------------------------------------------------------------------------------
Instrumented:   L.tenure
Instruments:    L.age cL.age#cL.age L.not_smsa L.union L.south
------------------------------------------------------------------------------
Gives the same results as the following CF model:
Code:
quietly xtreg l.tenure l.union l.south l.age cl.age#cl.age l.not_smsa, fe
predict cf, resid
xtreg ln_w l.tenure l.age cl.age#cl.age l.not_smsa cf, fe

Fixed-effects (within) regression               Number of obs     =      7,500
Group variable: idcode                          Number of groups  =      3,294

R-sq:                                           Obs per group:
     within  = 0.1351                                         min =          1
     between = 0.1783                                         avg =        2.3
     overall = 0.1770                                         max =          6

                                                F(5,4201)         =     131.21
corr(u_i, Xb)  = 0.1436                         Prob > F          =     0.0000

------------------------------------------------------------------------------
     ln_wage |      Coef.   Std. Err.      t    P>|t|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
      tenure |
         L1. |   .1755435   .0205221     8.55   0.000     .1353094    .2157776
             |
         age |
         L1. |   .0106753   .0070637     1.51   0.131    -.0031732    .0245239
             |
      cL.age#|
      cL.age |  -.0008867   .0001214    -7.30   0.000    -.0011247   -.0006488
             |
    not_smsa |
         L1. |  -.0452809   .0268467    -1.69   0.092    -.0979147    .0073528
             |
          cf |  -.1641325    .020582    -7.97   0.000     -.204484   -.1237809
       _cons |   1.671945   .1212711    13.79   0.000      1.43419    1.909701
-------------+----------------------------------------------------------------
     sigma_u |  .41441731
     sigma_e |   .2852065
         rho |  .67859444   (fraction of variance due to u_i)
------------------------------------------------------------------------------
F test that all u_i=0: F(3293, 4201) = 3.72                  Prob > F = 0.0000
However, if do not use lags in the first stage and lag the residual in the second stage instead, the coefficients differ.

Code:
quietly xtreg tenure union south age c.age#c.age not_smsa, fe
predict cf, resid
xtreg ln_w l.tenure l.age cl.age#cl.age l.not_smsa l.cf, fe

Fixed-effects (within) regression               Number of obs     =      7,500
Group variable: idcode                          Number of groups  =      3,294

R-sq:                                           Obs per group:
     within  = 0.1353                                         min =          1
     between = 0.1785                                         avg =        2.3
     overall = 0.1767                                         max =          6

                                                F(5,4201)         =     131.45
corr(u_i, Xb)  = 0.1454                         Prob > F          =     0.0000

------------------------------------------------------------------------------
     ln_wage |      Coef.   Std. Err.      t    P>|t|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
      tenure |
         L1. |   .2566965   .0304213     8.44   0.000     .1970547    .3163383
             |
         age |
         L1. |   .0144529    .006859     2.11   0.035     .0010056    .0279002
             |
      cL.age#|
      cL.age |  -.0013382   .0001577    -8.48   0.000    -.0016475    -.001029
             |
    not_smsa |
         L1. |  -.0346281    .027326    -1.27   0.205    -.0882015    .0189453
             |
          cf |
         L1. |  -.2452925   .0305005    -8.04   0.000    -.3050896   -.1854954
             |
       _cons |   1.710315   .1238945    13.80   0.000     1.467417    1.953214
-------------+----------------------------------------------------------------
     sigma_u |  .41454272
     sigma_e |  .28517027
         rho |  .67878182   (fraction of variance due to u_i)
------------------------------------------------------------------------------
F test that all u_i=0: F(3293, 4201) = 3.72                  Prob > F = 0.0000
Is it completely incorrect to do this
Code:
quietly xtreg tenure union south age c.age#c.age not_smsa, fe
predict cf, resid
xtreg ln_w l.tenure l.age cl.age#cl.age l.not_smsa l.cf, fe
instead of this?
Code:
quietly xtreg l.tenure l.union l.south l.age cl.age#cl.age l.not_smsa, fe
predict cf, resid
xtreg ln_w l.tenure l.age cl.age#cl.age l.not_smsa cf, fe
Sorry for a long post. I just wanted to demonstrate my reasoning with examples.