I've often wondered about this apparent inconsistency. I'm assuming it's a case of Deux ex Hollywood, but could there be a specific explanation for the fact that Transformers in the Michael Bay movies appear to accrue battle damage while in "robot" mode, that is not visible while in "vehicle" mode?
I'm aware, for example, that Bay's interpretation of Transformers meant they operated at a very low (molecular?) level, which is how their disguises are so good, even from the inside, so maybe the explanation, if indeed there is one, lies along those lines.