In 6.5.0 I added new rubble counters that you can adjust the level on so that you can rubble upper level buildings and the los tool will still understand that there is a higher elevation/obstacle in the hex. On the toolbar, click the cellar counter and then select the funky looking half-brown, half-green wooden rubble counter. Drag it on the map and then right-click and from the menu select the proper type (wood/stone) and level. It worked in testing!
Remember that LOS only works on RBv2 not other versions of the RB board.