Most PhD’s in university actually prefer to be called by their first name. As a graduate student, one of the most jarring culture shocks is to learn to call professors by their first names. At least that’s the case in the US, not sure about elsewhere
Without another name change, I don’t think that phrase will ever go away, for the simple fact that X as a name is too short and nondescript. In speech, X could refer to a someone you broke up with, or it could just be the beginning of another word, serving as a prefix. In text, it could refer to the actual letter itself, or the close button on a window, or a placeholder, or something NSFW.
There’s simply too many ways that X can be interpreted that even if people associate Twitter with X, people will still specify “formerly Twitter” just to avoid confusion