presumably you refer to the violation of individuals' rights here - forcing people to undergo some kind of cognitive modification in order to participate in society sounds creepy?

Out of curiosity, what do you have in mind here as "participate in society"?

That is, if someone wants to reject this hypothetical, make-you-smarter-and-nicer cognitive modification, what kind of consequences might they face, and what would they miss out on?

The ethical issues of simply forcing people to accept it are obvious, but most of the alternatives that occur to me don't actually seem that much better. Hence your point about "the people who do get made smarter can figure it out", I guess.