The GUI may call the same code although it doesn't call the same program. The AFNI gui program doesn't really call external programs (a bit different than some other programs out there), but I'm sure there are exceptions. In this case, the adwarp program uses several functions that are almost identical to the ones in the AFNI gui, adwarp_follower_dataset and adwarp_refashion_dataset versus AFNI_follower_dataset and AFNI_refashion_dataset in the AFNI gui.
For the second part of your question, the same question was asked very recently in this discussion.
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afni.nimh.nih.gov]