The public key is different for each enrollment, on purpose to deliver pseuonymity. If you enable U2F for Facebook, and then I borrow your Security Key and also use it to enable U2F for Facebook, although obviously that key will now work for either of us for signing into Facebook, Facebook don't learn that it's the same device. If Microsoft compares the data from GitHub to their own U2F data, they don't learn anything about whether GitHub users are also live.com users from that data, none of it correlates.