You are right; there have been two versions of ROMs shipped in the Macintosh
SE. The only difference, which also makes the two systems easily
distinguishable, is that the systems with Apple SuperDrives (formerly Apple
FDHD) have newer ROMs that include support for that drive. Those with 800K
drives have the original ROM.
Since the new code in the new ROMs is also used in the new systems, if any
incompatibilities exist, they are likely to be related to the SuperDrive
code and may very well affect the other Macintoshes with SuperDrives. We
aren't aware of any software compatibility problems caused by these new ROMs.