Pure speculation here: IF the auto bed is the culprit, it would make sense to put the same bed base in every rig to improve the speed of the assembly line and allow for a retro-fit if someone opts for it later.
You are thinking "mass production" where commonality is beneficial. I do see your point, but my thought is different.
Phoenix handles each rig uniquely, even units that are not made-to-order. Even if Phoenix made each model only one way, their offering of 9 different floor plans, still introduces too much assembly line variation when considering their limited production numbers.
I really don't think standardizing the rear twin beds would yield a benefit. But I will say that "for the most part" there are two standard modules that Phoenix favors. But even they vary.
1) The galley base cabinet with stove, sink, and hot water tank.
2) The B+ cap area cabinetry
I might be wrong, but I think Phoenix assembles every cabinet in their shop. One thing certain, they have to work very closely with their cabinetry component supplier or they would quickly end up with a room full of useless door & drawer fronts of different types of wood and finishes.