Well I looked thru the proc generated from afni_proc.py and this looks like the one that does it:
# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, mprage_ns+orig)
align_epi_anat.py -anat2epi -anat mprage+orig \
-save_skullstrip -suffix _al_junk \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-cost lpc+ZZ \
-volreg off -tshift off
There is no separate deskulling command. This is the first one (that I see) in the proc that does something about deskulling.
MIke