I think he's asking what happens if you have two panes side-by-side and try to select text in one to copy. Does it also select text from the other one?
I too generally use tmux's built-in text-selection and clipboard when I'm copying from pane to pane, because it's more convenient.
Or do the rotation thing. Or do the copy-mode thing. More than one way to skin this cat; just depends on which workflow you wish to adopt.