Profiles are next on the list of planned features, so they should be available on next fw version. They won’t be input specific, though, but there’ll be plenty of profile slots to use for saving various configurations.
My Neo-Geo AES os a neo-o (NTSC)
If you have a chance to try it with AV3 (e.g. via sync strike), it could work if it is same issue than with PAL Jaguar. Alternatively, if you have a scope and can post picture showing vblank portion of sync signal (like this), it is possible to verify if it’s the same root cause.