I think the thinking is that it discourages gaming the THC too much. The intent is that it encourages you to roleplay; picking and discarding thoughts just for the bonuses goes counter to that. It doesn't completely cockblock you however, there are situations where you might want to do that anyway and not just because you internalised a dumb thought -- for example, be a Superstar, level up your Perception, then make room for some other Thought.
I mean we are talking about a game that you have to pass "skill checkpoints" at key moments in the investigation to progress further, of course people are gonna "game" it, just like the clothing system