I found the IIsi and IIfx ROMs to be the same in terms of compatibility when used in conjunction with the Daystar Turbo 040 40MHz card. I didn't notice much of a difference when using the stock SE/30 ROM either. Most of the incompatibilities I saw had to do with the cache in the 040 -- some software just won't run at all or will crash, even if you disable the 040 cache in QuadControl.

The only difference I've seen between the IIfx and IIsi ROMs is that there are no horizontal lines at cold boot with the IIsi ROM. But you get the lines with the IIfx ROM.