Since the fixes MC-89760 and MC-82464 the compatibility with old non-transparent skin are broken.
See the jomo 's image from skin pattern (see above linked image):
The top right pink transparency detection square exist for compatibility reason (with non-transparent skin, like Notch skin, and only with 64x32 pixels skins). All others detections square can be remove.
See MC-89760 for more explanation about this bug.
Possibles solutions:
Apply the transparency detection only on 64x32 pixels skins
Apply the transparency detection only on the top-right 32x32 detection zone
The MC-89760 and MC-82464 fixes create more problems and impact more users than the original reported bug.
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@unknown In my opinion the better solution is to apply the transparency detector only on 32x64px skin, and disable it on new 64x64px skins.
This don't break backward compatibility and that solve the problem on 64x64 new skin format (the original reported bug).
In all case, I think breaking thousands skins actually in use by player is a worst solution that have a bug only on new skin. There are thunsands of old skins (without transparency) on skins websites, and players continue today to use theses old skins :S
I don't think any of the fixes you provided will be applied, it limits players from what they can do with their skin.
It's the skin owner's responsibility to make compatible skins, transparency and all.
If it's going to be fixed, then the first fix would be the best in my opinion.