When you "switch", you're telling your AVR what signal to send. If you tell it 7.1, it will send the Rear Surround signals to those 2 speaker outputs. If you tell it Atmos, it will send the .2 Atmos Height signals to those same speaker outputs.
Your AVR doesn't know what speakers you have connected to those outputs. To truly "switch", you'll need a pair of speakers located behind you for 7.1, and another pair of speakers located above you for Atmos. To "switch", you'll have to tell the AVR what you want, and you'll need to connect the proper pair of speakers, whether it's by changing wires or with a switch box.