True, however this speech finally comes in the last 15 minutes of the film, in response to Will saying something profoundly stupid, that he'd rather stick around and work construction than actually use his enormous talent.
It's also notable that this talk comes after (or near the end) of his sessions with therapist Sean and working with the professor - so he has come to terms with his past abuse (not claiming he is "healed" but he certainly is in a better place), learned a bit about structure from the professor, started interviewing, and now the final hurdle holding Will back is the intense loyalty to his friends. Chuckie not only gives him permission to leave them behind but tells him how stupid and disappointing Will would be if he didn't. He even tells him how to leave - just go, no warning, no message, no planning.
It's obvious this is something Chuckie has thought for years, but only verbalizes at the very end when Will needs (and is able to act upon) that final push.
Personally, I don't get why he has to leave. They are in Boston, obviously there's colleges and stuff, why can't he just do smart people things and hang out with his friends too. I feel like the whole "you must leave everything behind" is more movie logic than anything else.
Yea, well once Skylar moved to California his fate was to go chase her. You could call that movie logic, you wouldn't be wrong, but it's a lot better ending than "hey guys I got a job at <boston based tech co>, now let's go chase broads"