You have to remember that 3,2 will boot with a 3.1 ROM.
It will check the ROM version and try to remap the 3.2 system.
That doesn't explain why it takes so long to start up.
When you say SCSI is disabled, do you mean disconnected or entirely shut down on the Warp?
The Warp ROM startup will always be done before the startup-sequence, so if it is doing a scan of every SCSI address and LUN combination, that will take quite a while to check no SCSI devices are available.
Perhaps a terminator on the SCSI connector would definitely remove the issue.