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"Do any commercial orexperimental camera designs make use of such techniques?" I guess practical could also mean experimental cameras that were actually constructed and tested, as opposed to purely theoretical design ideas.
of course the RGB primary colors are different from the perceived colors of the bayer filters - that's because their function is different. color science is more advanced than "lets take a photo through a green glass and then project it with green light". this color difference has nothing to do with the need of demosaicing and with the reason why 2x2 RGGB grouping is inferior to more sophisticated algorithms. think of the foveon - no cross-pixels interpolation, we could say it is a pure subpixel grouping (like the OP wanted) and it works correctly. what's different, then? geometry.
OP specifically said the problem appears with tools acting locally so I guess global adjustments using curves probably does not break equirectangulars in rawtherapee?