Maybe it depends on the story? I can see your point about self-insert characters clearly representing themselves. In a lot of the self-insert fan fiction I've read, I've got a very clear picture of the writer's hobbies and interests.
But some can be really fun, I read a series about an interdimensional insurance agent, where the writer wrote himself as the most powerful man in the multi-verse. He later writes himself in again as an incarnation of himself the protagonist has to rescue from a comic convention. The series isn't meant to be serious sci-fi, so having the author lament those engineering classes he missed in college to the protagonist worked and made the story that much better.