When I have different HDD controllers in the same Amiga, I make one copy for each different device (I'm a simpleton), so I have an HDToolbox for the scsi.device and one for the gvpscsi.device (only the .info is changed with the device driver type).
You will want the most updated .device of each type (I use BoingBag #4 for the scsi.device) to get the drive size to show full capacity. The wrong capacity works (once it is formatted wrong), but that is a sucky solution (IMHO).