It should work. The driver for the FastATA automatically becomes 2nd.scsi.device because scsi.device is already taken. By this naming convention HDToolbox even recognises it without tooltype changes.
The default boot drive is selected by boot priority as always. You can give the CF card a higher prio than the SCSI drive if you want to boot from CF permanently. Certainly another boot drive can be selected for one session in the early startup menu.
