I think all those bogies are BX1s, so the whole train looks rather 313-ish to me. Did PEPs ride on BX1s at any point?
It would appear that the PEPs must have been test-beds for different bogie designs. Looking at the photos on the SEMG website, the 2PEP (from which the 25kV AC "3PEP" prototype was created) it would appear that this unit rode on BX1-alike bogies while the two 4PEP units had a completely different design not carried through onto any production units.
As for the door layout, I just guess it was decided to go for two doors per vehicle rather than three based on operational experience. Three door vestibules does rather eat into the number of seats. Perhaps passenger feedback was that seating was a greater priority than standing space. Either way, the reason would be lost to history. Unless you were there at the meeting when this was decided I don't think you will ever find out the reason why.
I've always been intrigued by the PEPs, especially the 25kV AC prototype. It's amazing to see just how many features were carried over into the production units. There is a YouTube link on the Wikipedia page, and it's strange to see how familiar the driver's desk. I'd never seen any photos of the AC version before, so my thanks to Dave for posting his photo of the unit online. It's interesting to see that, not only do the windows have no vents, but the prototype centre car has blanked-off doors so was clearly never intended to carry passengers.
A quick search throws up a photo of the unpainted aluminium car at
Ilford Car Sheds and another one at
Clacton Sheds.
O L Leigh