It’s not the lower/upper deck that is at different heights, it is the station platforms and doors. West coast has track-level platforms so the doors are on the

It’s not the lower/upper deck that is at different heights, it is the station platforms and doors. West coast has track-level platforms so the doors are on the lower deck, east coast has high-level platforms so the doors are above the bogies at the ends of the cars. Caltrain’s Stadtler trains have both sets of doors, presumably for future standardization on high-level platforms.