The fact there is a totally different way to copy text in the terminal is the issue, it just breaks the common mental model. Even worse, this shortcut _requires using a mouse_, and not just for copying, also for selecting!
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.
Any time I've seen someone do it it's: mouse to select, keyboard to copy, mouse to select other place, keyboard to paste.
I cringe every time because it could be just: mouse to select, mouse to select and paste it in the other place with one click.