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The solution you are looking for may be two Qtractor sessions open on two Qtractor instances at the same time.
In the automation session you can rename the Bus Master as "Automation" to avoid confusion and easily identify which instance is dedicated to automating and which is to be automated.

This would also simplify the organization of tracks. I would divide the work window into 2, Left (or Below) Automation, Right (or Above) Sound.
Hiding the time and other tools expendable in the automation instance would feel like an internal module created expressly to automate, even though it is not.