Thats funny you ask. Today I was attempting to put in a CD ROM on the same card. I was having bum luck getting both the HD and CD to be recognized at the same time. And then my HD died. So I removed the HD from the card and power/SCSI Cable leaving only my 8 MB of RAM. I booted with a floppy into WB3.1 to test your very question and had no problems what so ever.
You dont have to disable autoboot but it will speed up the search the card does for SCSI devices
So there you go...