Perhaps something got lost in the adaptation but is Homer supposed to seem slow or developmentally delayed? Did they cast the actor too old?
I found his character odd, he looks like he is 25-30 and has been in a informal medical apprenticeship for years to the point he is given duties in the hospital, yet he seems very young otherwise. His journey out into the world is something you’d expect of the mid to late teens though.
I haven’t seen the movie, but I read the book and it covers decades of time, and none of the things you mention are problem. My guess is that things got overly compacted in the adaptation to film. It’s a good book, give it a read.
Irving also wrote a book about the process of adapting The Cider House Rules to the screen: My Movie Business. It’s been awhile since I read it, so I don’t remember if he says anything related to the OP’s question, but it’s worth reading.
I thought Homer’s demeaner in the film was pretty on point for the character’s status as ‘raised-in-an-orphanage’ and ‘babe-in-the woods’ when it comes to the outside world. Especially since he’s supposed to be 20ish.