As it stands right now there won't be a compatibility issue with anything else at all, so you can stack away. I ran the original program (no longer being used) with the high-res patch, 9999 limit breaking, chocobo patch, transparent dialog windows, NPC-RP/PRP, even FF7Music and had no problems whatsoever. Given, the final release program will be completely different, but I still can't see there being a problem.
The only thing that could possibly cause a problem is something that alters the dialog on the levels. So if you use modified spell names and weapons, that's cool.