The master doesn't follow the project default track pan mode by design, instead it has its own setting, which is (now) stored with the project default settings.
The "linear scale" checkbox sometimes initializing as disabled is a bug that I can't actually reproduce but looking at the code I could imagine how it might happen, so we'll fix that.
I'm not sure what you mean by "reverted" at the end of your post. What was reverted?
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