You're just not quite thinking about this right. There's a big difference between game co-ordinates and screen co-ordinates. When you change an object's position you change its position in game co-ordinates. These are not the same as pixels on the monitor! All the scaling feature does is stretch what's in the game.
So for example: moving an object by 100 moves it in the game by 100 pixels. On a monitor 1000 pixels tall, this is 10% of the screen. On a monitor 500 pixels tall, the scale would be 50% due to the scaling feature, so it moves 50 pixels on-screen, which is still 10% of the screen.
The game happens independently of how it is drawn. Imagine you have no monitor at all! The game is still happening invisibly, and objects moving around in the computer's memory. Attaching monitors which display different parts of the game at different sizes does not affect those objects moving around in memory. So you don't need to worry about the scale at all when moving objects, or in fact in any of the game logic.