PFS3 supports whatever scsi.device can deliver. PFS sits on top of the IDE driver, it cannot extend the capabilities of the driver.
Without any patch, scsi.device supports up to 4GB (up zo 8GB with PFS3ds). With IDEfix or OS3.5+ it can handle up to 128GB. AFAIK there is no LBA48 driver for the internal IDE bus yet.
All that does not matter if HDToolbox does not recognise the drive as a HDD. You could try if it makes a difference to remove the IDEfix adapter.
Does the drive spin ? Sometimes even new drives have been in store for so long that the read/write heads stick to their park position. If you don't hear the drive spinning, you might want to gently hit it with your fist at the longer side.
Perhaps it might also help if you initialise the drive in a PC first and then put it back into the Amiga.
Bye,
Thomas