There's plenty of places around the Tokyo area where you have PEDs and mixed-stock: you simply provide PEDs for all train formations, and open the appropriate PEDs for the stock in the station. This would likely imply standardising the B07/09 stopping positions so that four/six car formations stop appropriately (i.e., a four-car would stop either at the same place or 1/3rd back). For some of the busier stations (Shadwell? Bank?) I'm honestly surprised there are PEDs: they're certainly very, very crowded in the peaks (and Bank is often bad partly due to people waiting by where the doors are open if it's the wrong destination!).
Good point, although I suppose it remains to be determined if that would be practical for such different arrangements of doors, there might not be enough 'null space' for doors to retract into on two different designs that both have their doors close together (compared to a regional/intercity train where the doors are sparse). I wonder if there'd be a way to build a half height PED that lowered into a gap on the platform and could deal with any door configuration, and whether this could be made safe for passengers.