You don't kick a national caliber runner off your team for doing jumping jacks or warming up on their own on an optional workout day.
I'm sure his coaches do hold a grudge about NXN. I probably would too if he skipped running with his team on the biggest stage in their own backyard so he could go drop anchor in a race he made a pact to do with his twitter-friends.
His coaches supposedly planning for him to do Footlocker is likely a load of bs as well. It's more likely that his coaches were being heavily pressured by Maton's parents to prepare to run FL and they could see that was the only way to keep Matthew and his parents happy. Then when Summit qualified for NXN, and would have been one of the top teams there with him, the coaches true feelings probably started to emerge.
This is a fail on both sides of the coin; the coaches and either Matthew or more likely his parents. Parent's need to let coaches coach without trying to pull the strings behind the scenes, and coaches need to be firm and not try to appease parents just because it's easier in the moment.
HS coaching is tough when you're dealing with phenoms.