I suspect having multiple -align_opts_aea is why you are not seeing the -giant_move option executed. I believe that you could use a combination of --tlrc_anat, -volreg_tlrc_adwarp, and -volreg_warp_dxyz to perform what you want in afni_proc.py.
If you're willing to use the nonlinear transform, you can use auto_warp.py once and then apply that transform to all of your afni_proc.py calls using the -tlrc_NL_warped_dsets option.
That said, perhaps you could clarify how you are warping the anatomic to standard space (are you using @auto_tlrc?) and what the eventual goal is. Why not include all of your runs in the same afni_proc.py call?
