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