Yes, it is compatible with all of those, as well as with the Unleashed difficulty hack. Most of them can be patched in any order. However, Alternate Fantasy has some special considerations:
Patch installation order (1.0 ROMs):
1. Alternate Fantasy v3.2
2. Comprehensive ATB Enhancement (or CTB Wait Addon)
3. Alternate Fantasy Compat Patch
This is needed because my patches overwrite some monster AI scripts to delete instant ATB fill gimmicks that would make the fights impossible, and Alternate Fantasy has tons of changes to AI scripts already. I should also note that I'm pretty sure Alternate Fantasy replaces/fixes Thunder Slash already.
By the way, it was recently brought to my attention that the AI scripts for all 3 fights against Beatrix have this issue if one of the conditions to end the fight (10 turns have elapsed or her HP drops below 10,000) while Freya is in the air, so that will be addressed in a soon to be released v1.01 of my hack.
