Another thought, you might use the shutdown sequence while all engines is still selected to not just stop movement, but get everything into a shutdown state before then going back to single engine operation.
Or leave them all running, your choice.
I gotta be honest- the same thing would be true in TMCC/Legacy.
You are just sending commands to all engines. The keep doing whatever the last command was.
If you want to stop them all, just hit stop in all engines address mode.
If you want to control a single engine- select it by using engine and ID