X has had two clipboards for longer than I've been using it, which is nearly three decades.

If your mental model of clipboard interaction only involves a single clipboard, and you use X, your mental model is simply wrong.

Sure, you could change X to match your mental model, but now you've broken the mental models of everyone who actually learned to use the software. And one more useful feature that makes X nice to use gets sacrificed to please the people who came from Windows but desperately want everything to work like Windows.