My own interpretation is that on the tactical map, they make no difference, but when you zoom in on a single band of merry adventurers, the internal seat is a nice upholstered bucket seat, and the infantry compartment is basically pillion seat except crappier and inside, and while the infantry compartment is budgeting for both seat and dude, seats are budgeting just for the seat.
Explanation example: so if you have hypothetical vehicle of 75 kg with 1 internal seat, vehicle is nice and happy. Stick a dude on it, it is now overweight.
hypothetical vehicle of 500kg and you add a half ton of infantry compartment. Vehicle is happy. Stick five dudes in it. Vehicle is still happy.