If, as I suggested on GitHub, the ".list Toolbox" was permanently moved to the bottom of the left sidebar, that would avoid the clutter over the map. The sidebar width would also be a good width for the Toolbox, since the entries are typically very short.
This would reduce the available room for the scrollable Waypoints list, but how many people use that? The Route Stats are nice to see at the top, but I wouldn't object to having to scroll a little more if I ever needed to use the Waypoint list.