These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
For reference, the communication music is known as "Wild Signals."
Listen carefully for musical Shout Outs to Jaws (when the mothership is communicating with the Devils Tower base) and Pinocchio (when Roy is being led into the ship).
The "voice" of the mothership was done by Jim Self, a legendary tuba player in his own right. Spielberg used him because the skill and difficulty of playing the tuba gave the mothership a "human" characteristic.
Harsher in Hindsight: Six years after Close Encounters was released, Colorado suffered a real toxic-gas spill following a train crash that forced an emergency evacuation, much like the cover story that was used in the film to justify evacuating the Devil's Tower area.
Hilarious in Hindsight: The humans who enter the mothership at the end are dressed in red jumpsuits and sunglasses, which in hindsight look like cheap versions of the aliens' outfits from the original V miniseries (in which the aliens did not turn out to be cuddly, friendly greys).
Although Roy never left his family, it was his family that left him! On the telephone to his wife, he says he is trying to be a good parent and that he'll do anything his wife wants if she were only to return, implying he sincerely wants to try to put his obsession behind him. Given the way the conversation ends however, do you think his wife was ever considering letting him see the kids again? Its hard to argue that Roy has anything really left for him on Earth?
His wife was angry and freaked out. And even if she still wanted to leave him when things calmed down, it's not like he'd never see his kids again. Leaving earth was leaving his family behind forever, no matter how you look at it.
He may not have left his family, but he certainly drove them away. Ronnie was freaked out and obviously at the end of her rope during the bedroom scene; when Roy starts trashing the house and stealing chicken wire, it's hard to blame her for getting the kids as far away as possible.
One way or another, Spielberg had clearly attended MUFON meetings and/or read their literature. This has happened to thousands of people who are or believe themselves to be contactees. Much of what Roy does, other than the sitcom whackadoo stuff with the chicken wire et al, is typical contactee behavior — the research, the night drives, meeting other contactees, etc. Looking for answers. Most spouses are supportive, but there will always be male and female Ronnies.
Spielberg himself has said that if he made the movie now he would've had Roy stay with his family.