I see "locked up in Flash" and "locked up in EME" as equal, so I'd prefer the one with more adoption.
The CDM API should make porting to multiple platforms easier because the browser implements all the non-DRM infrastructure like networking and playback. That said, I don't really expect Linux to suddenly be a top priority for Netflix or Amazon. On the other hand, a CDM is bright red bullseye for crackers. :)