I believe we are in a terminology conflict here. Let’s call Pinboard and TwentyFourtheen “themes” and the MediaElement.js polyfills “skins”. What I mean by default skin is how WP 4.0 styles the HTML5 video player by default. Pinboard theme uses a custom skin that overrides WP’s default behavior. It used to do this since WP 3.1 when MediaElement.js wasn’t part of WP Core. That’s where all the incompatibility comes from.