AFNI programs generally look in the AFNI binary directory (~/abin or /misc/prog/bin in your case) for atlases and templates, but you can put these datasets elsewhere if you want. Copying the dataset to your starting directory works for @auto_tlrc because that program does all its processing there in the same directory. afni_proc.py, on the other hand, creates a new directory and does its processing there. You could specify the full path to the base template to work around this difference as in "-tlrc_base /misc/prog/afni/current.x86_64/TT_N27+tlrc". Alternatively, set an AFNI environment variable to tell AFNI where to look for extra datasets -

"AFNI_GLOBAL_SESSION"
"AFNI_SUPP_ATLAS_DIR"
"AFNI_ATLAS_PATH"
"AFNI_PLUGINPATH"

Consider setting one of these in your .afnirc file in your home directory. The program, @FindAfniDsetPath can be used to check your settings. That program uses the same environment variables.