There are differences in where the display/USB ribbon connectors are and speakers are always in strange places. Sometimes the bottom tray is tapered off like a MacBook Air. Some ultrabooks are 9mm thick and others are 11mm thick, but at that point, honestly who cares?
But in general, I don't see any reason why a 13" standard for laptop motherboards+heatpipe can't exist. Out of the XPS, HP, and Asus systems I've upgraded in the last 6ish years, they've all looked more or less the same but with annoying 1-2cm differences in ribbon connectors and screw placements.
If anything, standardization might lead to more efficient use of battery compartments. A lot of laptops seem to have empty air surrounding a commodity battery that could have been 55Wh instead of 42Wh if the space was used better.
at that point, I have to wonder how much you would actually save by not replacing the screen, chassis, and storage. overall, this concept strikes me as more of a win for repairs than upgrades.