I think the problems were at corporate level:
#1. Ron Denis was desperate to regain full control over McLaren. He understand that this cannot be done as a customer team. Also, he knows that he doesn't have money to buy the Mumtalak shares. The only way to get money is to attract a big name in the automotive industry as works engine supplier, and a big name as pilot. Here Honda and Alonso are coming .
#2. Ron Denis is making wrong concept choice, so called "size zero", maybe for two reasons: a) attraction of PP, who is a big name in the aero guild and obsessed with aero downforce from his years in Red Bull (probably this assignment was also due to attraction of investors in Ron's corporate games); b) the wrong perception that Red Bull receipt for success with chassis is still valid (don't forget that the same mistake was done by Ferrari and Red Bull, too).
#3. Of course, the wrong concept didn't work, and the potential investors for Mumtalak shares pulled out. The Ron Denis days in McLaren were over, so the same with all connected with him, including Honda: they become convenient scapegoats. With one exception: Alonso who is enormous marketing asset.
Judging form the Amazon film, I think the decision for divorce with Honda was taken immediately after firing Ron Denis. The whole affair is not about the sport Formula 1, but about money - unfortunately we will never know the details of this story.
These are my two cents.