Why is it discouraged to disable the tray icon?

The Auto Dark Mode tray icon is the main control interface in order to properly stop the service. It also easily tells you when it is running and when it is not. Disabling the tray icon is a visual effect only. There is still a background process running when it is hidden, it is just no longer visible to the user.

Correctly shutting down Auto Dark Mode

When disabling the tray, you can only exit Auto Dark Mode cleanly by opening the AutoDarkModeShell and sending a shutdown command. The shell executable can be found in the same directory as the serivce and app executables.