The 8640 would definitely had been an option. It is a rather expensive ship, but still way cheaper than teh PA6T according to some AEon information which was about 500 US$ for each PA6T.
Plus Freescale is really helpful, they are still intersted to get their products out to the wild (genesi had and have a good support by them), other than PA Semi which is a company swallowed by Apple.
The 8640 has one or two e600 cores (aka g4) as known from the 7447A (Mac mini) or 7448 (some 3rd party cpu cards for Powermac G4). But it has a fast bus. Well, not as fast as the PA6T bus, but still quite fast, RAM interface is 600MHz DDR2, FSB is 200MHz (PA6T RAM interface is 1066MHz DDR, FSB is 233MHz).
But the difference of system performance between a PA6T and 8640D systen is probably only little. 8640D has the big advanatge of a proven and known core and a company behind it supporting it still actively. I was always in favor of the 86xx chips.