Yes this is a bit of an issue with the sequencer. Your solution is not a bad one, but still not ideal. I guess an eventual feature would be one of the sequencer slots (like the last one) is just empty and really the whole sequencer would be shut down for that slot. That would take a bit of work, so in the meantime you could just disconnect the MIDI start / stop messages.
In the patch there is a folder ‘CG-Library-Local’ and inside there is the sub patch metronome360.pd. You can open this file and delete these 3 connections:
This will disable MIDI from starting and stopping the sequence. Unfortunately not the best solution because you will have to do it for each patch.