My advice would be that your son not you initiate a conversation with the coach and the subject would be what do I have to do to improve and make the team as I want to play and help the team win?
Hopefully that conversation clears the air and your son gets through his Senior year and moves on to play at next level. Depending on the feedback and outcome , you can then determine next steps.
He might as well try to clear the air first , because coaches want to win and if he is as good as outlined above , the attitude must be a huge issue in this coach's mind so much so that he would rather him not there around younger players. Not saying the coach is right in his view just pointing out that most elite players don't get cut.