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?
If you use a mouse yeah, but as noted by others, with tmux 1.8+ just prefix-z and you can temporarily zoom that one pane. So there really isn't much reason to complain about this particularly.
Well, this is not really the dilemma though. If you don't have vertical splits you don't have this problem, but you also don't have vertical splits. If you have vertical splits you'll solve this problem somehow.
They're talking about using the host terminal's text-selection mode and the system clipboard, rather than tmux's built-in text-selection mode, which does.
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.
The thing is you can synchronize tmux selection with your clipboard, there isn't really a need for tmux to "support" your terminal's view of tmux running within.
The answer is, it depends. If you copy it with the mouse, you will be copying both sides. If you copy it with your tmux keyboard copy bindings, it will copy just the one side. I don't know the default bindings because I made mine prefix-esc to get to copy mode, vi keys, v to select, y to yank.
