Nothing is being overridden. You have apparently misunderstood copyright licenses as being something that attaches to a copyrighted work and now must be respec

Nothing is being overridden. You have apparently misunderstood copyright licenses as being something that attaches to a copyrighted work and now must be respected by all users of that work. But that is totally incorrect. Licenses are individual agreements between copyright holders (or licensees who have been granted the right to re-license) and people who want to exercise one of the rights normally withheld under copyright. A LICENSE file is nothing but an offer to grant a license with specified terms to anyone who might want to use the work, without having to nag the licensor to sign an agreement. The existence of that offer doesn't have anything to do with any other agreement the licensor and a (potential) licensee might make. In the GitHub case, GitHub has negotiated a different license with the uploader. (That negotiation happened to take the form of a ToS, which is another kind of binding offer.) The LICENSE file has nothing to do with it. It hasn't been overridden, it's just irrelevant. It doesn't add or subtract any terms from the separate and distinct license GitHub negotiated.