Hello, from what I know, there should be no issue with tossing them on roofs. You can usually throw them onto any floor and they do not normally mess with walls or foundations. I can say that they should not be any different in CFE true or false and should do nothing to floor elevation so I do not understand why they would come foundation height.
The only thing I can suggest is to turn the frieze cheat off. It should normally do nothing but just in case. Other than that try restarting the game, which should reset any cheats you are utilizing. Did you try using the tool normally in a new lot or anything and does the same thing occur. If the same thing occurs after a restart then I am totally baffled lol, sorry.