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.