But the issue you raised is valid. Displaying 2 different layouts for different displays connected to the same system might not always be productive.
Layout muscle memory issue needs to be addressed in some way in multi monitor cases. Installing / removing apps also leads to minor layout change, but the user can always fix the new layout in his end. But, in case of automatic layout grid adjustment ( 8x3 ↔ 6x4 etc ) when switching displays, the user cannot do anything.