If he starts three years in college, he literally has nothing to gain in draft stock (beyond hoping you "roll for a weak QB class" deal) and LITERALLY everything to lose in terms of injuries. This year was a weak QB class and Watson didn't even get drafted first in the QB pool.
If he starts three years here, he should leave regardless of the draft stock because it is unlikely that he's going to unlock some magical knowledge or height-growing serum in one extra year. btw, this is assuming he's a 3-yr graduate type.
I don't buy that. NFL minutes are hard to get. There are a lot of things someone can work on in their 4th year of playing that they can't do as easily in the NFL. There are also plenty of guys who needed that fourth year to become a high pick. I'll concede that a player can hurt his draft stock by exposing himself a bit in a fourth year (Tim Tebow and Matt Leinart come to mind), so without a doubt I'd say that if he somehow ends up pegged to go high, come out. That part isn't up for debate.
It sounds more like you are saying that he can't hope for much so he should take what he can get. I can think of a lot of guys who would have benefited from extra polish on their game. Manziel left early, and he darn sure could have used a lot more development. He got drafted early enough, but I can't think of how staying another year or two could have possibly made things any worse, that guy was a train wreck (and might have been either way). There's a lot of guys who played a lot as freshman yet really helped their stock in that fourth year. RG3 flipped a switch in his fourth year, and remember he threw for 2,000 yards as a freshman. No question sticking around benefited him. What about Russel Wilson? He threw for 1,955 yards as a freshman, decided to stick around for a fourth year, it was a monster year, and we know how that worked out.
The fact is I can find a lot of quarterbacks that benefited from a fourth year, and quite a few that would have, at least in a developmental sense. Now, I guess you're just being really cynical. That his draft stock won't get higher after his third year, so take the money and run. Or you're being really positive, in that you think he'll put up monster stats and there's no way he can top that. But, there are plenty of scenarios in which a quarterback benefits from a fourth (or fifth) year.