It should fit there in nicely. The spacers are quite long between mb and pci busboard, ie. there is quite a lot of room even between big battery and busboard.
Excessive heat is never good, so you can add small fan blowing air between busboard and motherboard to keep things cooler.
You can also consider external scandoublers, or even
this which I recently bought for 88 euros (haven't arrived yet) and which has gotten quite good reports under amiga usage (works as scandoubler, flickerfixer, is compatible with high native resolutions, handles all the 24bit colors etc.) with good cable. There should be some topics about this even here.
