I've finally tried emacs's cua-mode which lets you use ctrl + x, c, v, z for cut/copy/paste/undo (i.e. like the rest of my desktop).
And it's surprisingly nice and not disruptive at all. All the shortcuts (like "c-x o" or "c-x c-f") still work as expected, but you get a more consistent clipboard approach.
The mode is really well implemented and fits in much better than I expected.
The only thing I had to adjust to is to stop scrolling with ctrl + v / alt + v and use the Page Up/Down keys instead.
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