Hmm, this is a bit confusing. Should it really be an option?
I mean Alpha in the context of Principled BSDF shader is basically the amount of physical presence of the material in the scene world, which can be specified on sub-triangle basis, by the texture. I am having a hard time imagining use case where someone would want to have some AOV data present in the areas where the object is masked out (and therefore reveals some objects behind the masked areas). Such AOV would then end up unusable as it would be also modifying parts of the other objects which are revealed by the non-1 alpha masked areas.
If it’s going to be changed, I don’t think it should be an option.
It’s also a bit concerning that task is now over 2 years old, and Cycles still can’t do something as trivial as baking a texture of a tree twig