How can I change the order of displays in the app menu?

Set a Custom ordering string for each display or virtual screen you want to reorder. The app uses this text as its alphabetical sorting key without changing the display’s visible name. Values such as 01, 02 and 03 are an easy way to establish an order.

For a physical display, open Settings > Displays > [display] > Additional Settings…. For a virtual screen, use Custom ordering string in that virtual screen’s settings. Set ordering strings on all devices whose relative positions you want to control, and check the resulting menu.

Virtual screens without a custom ordering string normally follow physical displays. Giving a virtual screen an ordering string allows it to sort among the physical displays. If Settings > Menu > Show main display at the top is enabled, the main display keeps that priority above the ordinary ordering.

This changes menu order, not the desktop arrangement or where the pointer crosses between screens. See Additional Settings and Virtual Screen settings for the corresponding preferences.