That internal SCSI port is the same chain as the external, same speed. The older Powermacs had dual SCSI one for external 5mb and one internal (10mb?).

Anyway running a SCSI drive with the native SCSI chain would be very slow for an OS drive.

http://www.lowendmac.com/ppc/beige-power-mac-g3-1998.html <=== list a 4gb UWSCSI so they must have bunfled it with a PCI card.