I believe they settled it by paying some royalties on Commander Keen.

A lot of times Carmack just wants to get shit done. At Oculus he has worked on both the Minecraft code and the Netflix code both for VR clients, both (I believe, I know for sure for Minecraft at least from some talks) with MS and Netflix retaining full ownership of the code.

Maybe they have some "off the record" agreements to avoid anti-trust--Minecraft still hasn't officially come to Vive.