It's not just about two independent panes. It's about two panes in a single context. With this, there can be shortcuts that act in files and which now don't just have a source (the selected files in the active pane) but also a destination (the inactive pane), so copying, symlinking and moving all can be done with a single key without the need to provide a destination.

Two explorer windows are independent of each other. Any move or copy requires two keyboard actions or the use of the mouse

You could in principle setup shortcuts the same way (treat right tab/second window as the automatic destination), but that'd definitely be more error prone vs a built-in dependency