As best as I can tell this is all over a trademark dispute over the "WP" in WPEngine (and a hand-forcing by Automattic to implement a retroactive licensing agreement)?

Not just a retroactive agreement, a retroactive rewriting of trademark usage. Up until a few days into this dispute, the appropriate text on WordPress's site explicitly permitted people to use "WP" as they saw fit (as much as they can, as I don't believe they have a trademark on WP, just WordPress). Matt hastily edited things to imply WPEngine was in violation.