An offer from Microsoft to "certify" a third-party application for Windows is simply an offer to test it to make sure it works. I'm not defending Microsoft or anything, since limited effort is extended to make things like games "certified," but this Notch guy seems like he goes out of his way to be difficult to deal with. Either that or this tweet could be translated as "Screw you, I hate Windows."
Personally, I'm going to skip Win8 like I skipped Vista. And I don't care about Minecraft.