I'm also not sure if I like the implication that Roy is transformed into an alien. It brings the Pinocchio reference full circle I suppose, but , I prefer the ending to have some mystery to it. I also think these scenes hurt the pacing a bit.
I'll have to rewatch that scene, because I don't recall ever getting that impression.
I also don't care for the mothership interior ending. While it was technically impressive for the time, it's something that didn't need to be shown, and was obviously tacked on as an incentive for people to see the film a second time in 1980.
Regarding Roy's family, I have the director's cut DVD, and Spielberg says in an interview (on the set of Private Ryan) that if he made Close Encounters again he wouldn't cast the family in what was essentially the villain role and have Roy leave them.