Open steam and launch the FFVII launcher. I haven't tried loading up a save to see if it grants retroactive achievements, but I have tested opening a modded save through normal Steam gameplay, using a limit break, and got achievement credit. So Steam can't see and record achievement progress. It doesn't launch the game via Steam but rather through the mod manager itself. You miss out unlocking achievements and cloud saving due to the way the game is launched from what it seems to me at least.