For instance, I'm very thankful that my text editor and terminal allow me to split panes within their window rather than through multiple instances handled by the OS. I seem to prefer having panes/tabs vs window instances when alt-tabbing. Especially if I have two browsers splitting my viewport and a couple full sized browsers. This makes it very annoying to alt-tab only between the two half screened browser windows. On OS X anyway.
I actually tried using OS X's full split screen, but that creates a new virtual desktop. And even with reduced motion (which helps a lot avoiding headaches when working on multiple windows), it's still too slow/animated for me to switch between my virtual desktop with split screen browsers and other virtual desktops with editors/terminals etc.
Finally, what's nice about split panes vs window instances is resizing. Resizing one pane resizes the others. Whereas resizing one window does not resize the others (at least not on OS X's default floating windows. But even something like Spectacle. Someone knows of a tiled window manager that resizes all windows when resizing one btw ? Looking for something like dwm for os x)