Lee’s argument, as I understand it, is that switching between windows in a single frame is suboptimal because various Emacs operations will destroy your windows configuration and using something like winner-mode to restore your window configuration is too much trouble.
I’ve been using a single maximized frame, split into several windows, and I’m frequently frustrated when I trigger some action which fouls up my carefully constructed layout. I’ve tried “layouts” and “winner-mode” and still never feel like I can predict window behavior. Lee’s suggestion to use two frames, side-by-side, has greatly improved the way I feel using Emacs. He’s right, it’s better this way.