I agree. And whether or not Automattic gets the money or WordPress.org does matter, but so does the way any such transaction is structured.
If Automattic is an infrastructure vendor (in a technical sense at least) to WordPress.org, it’s still reasonable that Automattic doesn’t want to just give its competitors free infrastructure.
I own a hosting business that’s heavily built upon WordPress and even I — at a scale immensely smaller than WP Engine - CDN some of my critical plugins and themes myself. (For a lot of reasons.)
WP Engine is absolutely massive. The load they put on systems that they consume from isn’t trivial. Asking for remuneration from a competitor that is using your services, according to their means, isn’t anticompetitive.
The fundamental question is: is the non profit going outside the boundary of its status?
I’m not fully convinced that’s the case even in the context of the for profit disagreements with its competitor.