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I think the behavior that the user expects on an intuitive level is:

If the track has been created or modified with "auto" checked, when it is opened it must be checked. The same goes the other way around.

What this means, as Rui comments, is creating an individual track property, like any other property (selected midi bank etc...)

Now, is it worth implementing it?

As it is now it is functional, although it is true that it creates a certain strangeness.