Good news, the mystery is mostly solved. The weird HD20 disk corruption problem was specific to that one SE/30. With a replacement ROM in the new SE/30, Floppy Emu HD20 worked great.
I also confirmed my earlier theory about certain RAM causing problems for any IIsi or IIsi-derived ROM in the SE/30. This behavior was consistent in both SE/30 machines. There is a particular set of 4 mismatched 4 MB RAM SIMMs that work fine in both SE/30's with the stock ROM, but won't boot in either SE/30 with the IIsi ROM or the BMOW ROM. I spent quite a while swapping RAM and ROM between the SE/30's and other systems to convince myself this was a real effect. I know Techknight said he's seen cases where the same RAM worked with the dougg3 ROM in one SE/30 but not other, but my hunch is there was some additional problem at work there.
The troublesome set of 4 x 4MB RAM was this:
USA SY 9304, 4P1004JDJ-M8
81C1000A-70, 9418 F64Z, Malaysia PJ
AAA1M300J-08, NMBS 2091
TI-80, TMS4C1024DJ, HEI 114A R