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Shared layers do behave the same in all the canvases that share them.

They don't have to appear in the same order in all canvases, though. That lets you mask the ones you want disabled in a particular canvas. Put all the shared layers you to be invisible at the bottom of the layer stack in that canvas. Just above them add a layer completely filled with a background color (i.e., a strokeless filled rectangle the size of the canvas).