Some years ago, in the late 2010s, I worked for JDA Software, who specialise in supply chain management. (They are now called Blue Yonder and are owned by Panasonic.) They developed an InDesign plug-in which did exactly what is being requested: it allowed you to create groups, or sets, of layers, and any layer could belong to more than one set. You could manage sets just as you manage layers: lock them, turn visibility on or off, output them separately etc. Also, sets themselves were nested, so could contain other sets.
In their application, it was used for constructing advertising for retail supermarkets, either printed as inserts for newspapers or published on the retailer's website. It made production efficient where a large grocery chain has multiple "price zones". The products advertised are mostly the same across all the price zones, but sometimes vary. In some cases, the price of a product might be different in certain price zones. In some cases, a product would be replaced by a different product in some price zones. And sometimes, advertising in a certain price zone would require a different legal disclaimer. The layer sets allowed everthing that was common to appear only once, but then be replaced for particular price zones. For example, the grocery chain may be allowed to sell beer in some states and localities, but not others, so those ads would need to be replaced. Or they might charge more for the same product in one state or locality than another. I installed the product at one grocery chain which had 70 such price zones.
It was extrenely useful and I can think of many other applications for it. But the important point is that it can certainly be built, even as a plug-in. Pity no one at Adobe is listening. I wish someone would develop a plug-in, though!
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