> The SAM460 had a V1 PCIe slot?

Yes, and it still has ;-) The PPC460EX was introduced in 2007 half a year before the first PCIe v2 hardware came to market.

> If [...] it's not a 1.1 or 2.0 slot [...]

PPC460EX of Sam460 has PCIe v1.1 (same as PA6T of Nemo/X1000), while CPC945 ("U4") of PowerMac11,2 has PCIe v1.0a (same as P1022 of Tabor/A1222).