They're just afraid you'll asplode another Admiral.
I don't know, are there some bits of the Naval Academy that have you in a Type II? Would Commander giving you a Type VII sized crew be a problem if you tried to load a training/tutorial session that used the smaller boat?
But I have to say, I've used several of the Academy tests to do a quick test of various mod combos, and no matter which one I chose or which career I picked in Commander before launching the game I've never gotten that particular message. And almost all my careers in Commander have been in a VII so you'd think that if crew size disparity between different boats was an issue I would've come across the error by now.