Not a bad idea. You definitely don't want people getting "load" and "merge load" mixed up.
Maybe even skip the separate button, and have merge load just a checkbox on the load menu?
The Presets tabs do that already, so I'd suggest doing the same thing for scene loading. But maybe it should automatically clear each time, as accidentally merging different scenes together might take a long time. Merging hair or clothes by accident is not nearly as bad.