FWIW, I do believe that I have seen something that lead me to believe that there are more than one PCI Bus in Compaq Servers. In fact I believe that there are usually three, in modern ones, (Not counting ones with PCI-X, I haven't seen any of those) a 64 bit 66 Mhz, usually 2x, one 33Mhz, 32 bit and all the rest 64 bit 33 Mhz.
I think there may be a fourth for internal SCSI drives, as the server in question had an add in board, that looked more like a Mini PCI board than anything else, and added RAID functionality to the onboard SCSI controllers, (wether that was a fourth PCI, or something else I couldn't say though.