As I understand it, it the commercial/naval split has to do with the pacing of the game.
The balance is that about a 10k ton naval ship at the start of the game is about average. However, that system falls apart when you throw in the needs of commercial ships - heavy, bulky, cargo holds and long-range engines. So if you had a 50k ton commercial ship - not uncommon at the start - that was suddenly made into a military design as well, that spoils the intended pace of the game. Also, commercial ships are more likely to be working all the time with loop orders, unlike naval ships which may just sit on defense. Commercial ships don't have to deal with naval maintenance and morale.
But that's just my theory on the reasoning behind it. Perhaps some of the veterans around here or Steve himself could explain better.