What an odd vertical contraption for AGP and PCI cards... Why is this necessary?
It's not. It's there to allow placing the motherboard into very thin case. Normally the PCI and AGP cards add lots of height to the machine, and if you want to place the mobo + gfxcard + few pci cards into very small case such riser cards is necessary to get the cards vertical.
And why is there such an odd little PCB in the outermost PCI slot?
It routes some of the needed signals of the 2nd PCI slot to the riser card. So that is part of the riser card, not Pegasos itself.