I was comparing the old special run from Prototype N Scale to the new Atlas car and got to thinking...
So if the MTL PS-1 body is too high, and the bottom door track should be lower, but the door is the correct height... (See Atlas PS-1 thread)
Then why not just chop off the sill tabs, carve new sill tabs into the old sill, and call it a day?

Modified sill on the right.

Modified MTL compared to new Atlas.
Somebody good at CNC milling could work this up to be modified in a single setup. And the same setup could move the floor farther into the body and set it at the right height. Aztec should take this up now that decoder frame milling is unnecessary!
(I don't know where the "The" on the Atlas car ended up. It was on the pre-production cars. Either I got a misprint or a new error got introduced when they corrected the word Compartmentalized.)