A related article that came out today about how Dolan resigned from the BoG with a bit of a tantrum back in July.
https://www.espn.com/nba/story/_/id/...ttee-positions
The coach was only hired by the Raptors on July 25th and most of the actions cited in the lawsuit happened in August, so in light of that, it really sounds like Dolan is just pissed at Silver and the other owners for things unrelated to the Raptors (particularly revenue-sharing), and is making a stink about this minor infraction just to make a point of being belligerent.
The league bylaws are really clear that Silver has absolute and final jurisdiction over any dispute between league members. The fact the Knicks made up a damage amount that's greater than what Silver can award doesn't mean that it's therefore outside of the commissioner's jurisdiction.