I want to add something to this in that alpha blending seems to be related to the "background geometry" setting in models. I think this setting is responsible for why the skybox is still visible in Figure 1 of the original post but I'm not quite sure, so I'll describe my situation:
I had basically several flat meshes behind each other with textures A, B and C. They were ordered A B A B C with C being the skybox with no alpha channel and A and B both having semi-transparent parts in their alpha channel. In my original setup, neither of these meshes had the "background geometry" flag enabled (not even the skybox C).
In that case the skybox would always render in the background behind the semi-transparent parts of A and B. If A and B occluded each other however, only the one with the higher alpha blending would render through the semi-transparent parts of the other. So if let's say A has an alpha blending of 1.0 and B one of 0.9, then I can see A through B but not vice-versa. If they both have the same alpha blending, it would still favor one of them. This seems to be related to the model hierarchy as described by JC here. Basically, they have to be linked to the base from back to front for the semi-transparency to work properly.
Things changed however, when I changed the "background geometry" setting. I originally activated that only for A and B as I assumed that C already had it enabled which turned out not to be the case. Once I did that, the alpha blending for A and B no longer mattered. Both A and B would now be rendered through the semi-transparent parts of each other. But now C would no longer render behind them. Once I enabled "background geometry" on C as well everything worked as intended. Now all meshes are rendered behind semi-transparent parts of all other meshes with their alpha blending all set to 1.0.
So maybe "background geometry" is some kind of override for alpha blending in that meshes with that setting enabled are always rendered behind semi-transparent textures but if they themselves are semi-transparent, no non-background-geometry-mesh is rendered behind them.
Maybe this can help in some instances where only changing the alpha blending value doesn't work.