That defeats the point of using the "parallax in editor" setting. The point being is that it is suppose to allow you to work on a layout with parallax layers more accurately and efficiently. With the setting turned off, everything is guess work. You can't know where an object is going to be, in game, so you have to constantly test the game to see if things are lining up, or turn on/off the setting all the time for each layer.
Ultimately this results in a lot of tedious nonsense, and makes working on a game with parallax backgrounds a nightmare.