The rear compartment does change, the VIIA has a little desk while the B/C/C41 have a alarmingly always-open torpedo tube.
In real life there
were differences in the internal layout of the A and the other boats, but I can't remember off hand if they change so drastically in game. I doubt it, if only for the fact that you'd only be using the A a short time so the time and resources to fully model it wouldn't be worth it.