I think it's good to have the asm inc files organized in a similar way as the C inc files.
I don't see a cbm.inc, so I cannot follow your c64 example.
And I strongly believe one definition (e.g. register layout) should only be in one place.
I'm fine with renaming _xxxx.inc to atari_xxxx.inc, but apart from this, what else don't you like?