I don't remember this happening with the SCSI drives from My A3000 and A3000T
HDToolbox always sets the "last drive" flag on the drive with the highest unit number.
If it works or not depends firstly on whether the driver recognises and respects the flags and secondly on the order in which you add harddrives.
If for some reason on SCSI you started with a high unit number and added drives with lower numbers, then the oldest drive always stayed the "last" and you never had to change something.
The flag is made to speed up boot processing. If you keep partitioned drives with low unit numbers and non-partitioned drives with high numbers, then drives without partitions (CD drives, tape drives, scanners etc.) are not checked for partitions at boot time.