I tested the external FW800 drive as a scratch drive against the internal, using the DigiLloyd tools, and the internal drive won by a wide margin. So, yes, the internal SATA drive has a faster connection than the external FW800.
However, scratch is different from image storage and use. I don't know that any lower speed will be noticeable, especially if I leave my Lightroom catalog on the internal drive.
This issue is why they still sell Mac Pro towers, of course. Plenty of fast, cheap internal drives, more RAM, etc.