Which is an implied contract, yes. Which a court would probably find that Mojang have an implied license to use the poem, yes.
But the terms of that license are unknown - a court may well decide that it did not apply to Microsoft since he didn't sign that contract. And it also means that he did not assign copyright to Mojang or Microsoft which removes that avenue of them claiming they can use it for free.
Ready his comment again. It does not matter because Mojang still exists, it's just a Microsoft-owned company now. The contract and everything else related to the game is still property of Mojang, nothing has been transferred.
A court may well consider that becoming a wholly owned subsidiary would violate a license, despite being a distinct legal entity[1][2]. Especially when it's just an implied license with no actual agreed definition on both sides.
[1] Which is similar to what we're seeing with ARM vs Qualcomm and it should be interesting to see how that shakes out.
You’ve linked an article about a doctrine specific to patent law. Does not apply here. Also, it only speculates that it might be in issue in an acquisition of a subsidiary (vs. a direct merger).
But the terms of that license are unknown - a court may well decide that it did not apply to Microsoft since he didn't sign that contract. And it also means that he did not assign copyright to Mojang or Microsoft which removes that avenue of them claiming they can use it for free.