Mods made for the AA2_MAKE profile will work with the new profile. If you only install the profile it is recommended that you delete \_generalgame_profilesAA2_MAKE.pro to avoid accidentally selecting the wrong profile.
Known issues
Sometimes when applying a mod a question appears asking what type (see screenshot below). Just click OK. It's a "feature" of PPVerDecrypt and I dunno how to fix it.