Exactly. Host keys are about authentication, not connection security. Presumably the upthread comment is trying to say that "ssh communication with github could have been subject to an undetectable MitM attack by an attacker with access to this key"[1], which isn't remotely the same thing as "all communication with GH since the founding of the company has to be considered compromised".

[1] Which is sort of tautological and silly, because that's true of all sites and all host keys. What the comment was trying to imply was that the choice of storage of this key invalidates any trust we might have in GitHub/Microsoft regarding key management, and that therefore we shouldn't trust them. Which is also tautological and silly. Either you trust them or you don't, that's not a technological argument.