Main stage 3. How to stop metronome when playback ends?

You just need to use the "Stop" transport command. You can map it to an external controller if you like.

Remember, a Mainstage Concert can be in Play or Record mode which starts the concert level MIDI clock. That's a totally separate function from the playback plugin, which "stops" when the file ends. But until you hit Stop within Mainstage at the concert level, it's still ticking away.

Direct answer: Correct. Mainstage will not stop the main MIDI clock automatically.

Easy solution: Hit space bar at the end of each song, or both metronome and stop commands can be mapped to whatever hardware you are using.

Harder solution: Automate Mainstage using an external application (such as Logic) that will stop it automatically at the end of each song.