The use of which were already allowed under the existing open source licenses...
In other words, a shakedown by another name.
Also, suggesting that WPE's contributions to the non-profit could be satisfied by paying Matt's for-profit company is almost the textbook definition of private inurement. I don't think he had lawyers familiar with non-profit law clear that offer before he made it. If I worked for the IRS right now WP and Matt would be pretty high on the list of organizations to take a closer look at.
Can you be more specific about where the WordPress licensing grants the trademark usage WPE is using? WordPress is GPL2, which doesn't have a lot to say about trademarks.