So I did some more testing with the BlueSCSI v2, and I believe the issue is the transceivers or buffers are asserting control lines as the SCSI controller initializes, because the SCSI controller initialization is happening before the RP2040 finishes initialization.
Here's the BlueSCSI v2 startup:
Here's the original Conner drive for comparison:
Zooming out a little on the BlueSCSI from wake:
It's around 330ms until BSY de-asserts. I believe that's around 5 million clock cycles at 16MHz, or maybe 200,000 CPU instructions.
Here's what happens with another device on the chain providing termination externally:
The moment the BlueSCSI gets power, the transceivers assert the control lines.
And for another test, here's what happens when you have another device on the chain, put the Portable to sleep, disconnect the BlueSCSI then wake from sleep:
If you reconnect the BlueSCSI at this time, everything works as normal.
I'm guessing if you could just keep the transceivers/buffers from asserting SCSI lines until the RP2040 is ready or delay their power up, it would likely resolve the issue.