From my experience with an A3000 system, upgraded to all the latest custom chips (rev 9.03 motherboard, dmac 4, ramsey 7, WD-SCSI-08, Buster 11, KS3.1) and an A3640 card in it:
Rock solid performance when using the stock SCSI controller.
SCSI troubles if using the stock SCSI controller for some devices and let's say another SCSI controller such as CSMKIII SCSI for other SCSI devices (i.e. running two SCSI chains), if I take out the A3640 card and use the CSMKIII instead.
Of course, proper libraries are installed for every combination mentioned above and the INT2 fix has been installed on the A3000 mobo.
In other words, A3000 SCSI has never played along nicely for me if I introduce another SCSI chain to the unit, If I only used a single SCSI chain...I've never had a problem, even if the chain were from CSMKIII, but two at the same time gave unreleable operation.
I've never had any grief or complaints about the A4000 operation though. :-D