There are only two things I think it could be given your extensive and very well thought out troubleshooting. 1. There is liquid damage that is not seeable. Perhaps on the opposite side of the seeable motherboard or tucked away in a corner. 2. The LCD has gone bad (somehow) and it would need to be replaced. Seeing as that this is a retina MacBook an LCD replacement can be expensive. If you're willing to take on the challenge of taking out your motherboard I would take it out and look for any signs of moisture, especially around the display connector. If you see any, anything at all, take a soft-bristled toothbrush and some Isopropyl alcohol and scrub it clean.
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