Yeah, when things are stacked Z-Order has to take precedence because (obviously) there's no other easy way to define a default target for something like a paste operation other than to assume that what's on top of the layer (or what has the current edit focus) is the target.
But it's easy enough to do that, selecting a note on a clip brings it forward, makes it the active target, much the same way it works in Reaper now if you cut a note from clip A, select a note on clip B to give that clip the edit focus, and then paste.
Same thing... for cut and paste moves.
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