If by “stacked” you mean “z-stacked” (as opposed to “y-stacked”), the only thing I’ll say is that the former approach opens the possibility of layout issues, as I learned when assisting with this post. (I created a simple demo/test page.) A former z-stacker, I now y-stack all of my initially hidden elements. I don’t use a ton of reusable elements, though, so I can’t say if/how things might differ in that context. Needless to say, the editor page can get pretty long, but navigating the editor by clicking elements in the elements tree (as opposed to scrolling) is still quick and snappy.
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