Simple work around. Put the light fixture in the same spot on both floor views.
NOW, find another area where you have a 3 Way Switch and Copy and past that switch where you want it on each floor. Click on the wall switch and "Open Object" Uncheck the box labeled " Automatically Change Switch Type When Wiring".
Now wire each switch to the light on each floor and in the plans, it will look like a normal 3 Way Switch Schematic.