Maybe the Foundation has some sort of contract (written or non-written?) with a 3rd entity (the "Rust project", whatever that is)? If that's the case, then this could restrict the Foundation's power, even if the Foundation holds the mark.
Now I'm really puzzled, and I would feel greatful if someone could help us understand. See also What is Rust / Who owns Rust?, which I posted a while ago.
Maybe I'm thinking too complex, and all these legal matters aren't really sorted out and it's all a big mess?