...
I have tried to read the walls of text that this thread had and, well...
Ow, my head... it's pounding from the text... Need to rest my eyes..
Anyway, I want to put in something silly(although still possible, IMO) as a partial explanation for all of this...
Simply put, no one has noted that space time jutsu is what made Tobi's little "ghost phasing" jutsu and the Kamui technique(I am not going to argue about whether they are the exact same or different or something, that's not the point here) work. I also know that Minato also uses space time jutsu as well...
My wager is that a space time jutsu is what allowed Obito to survive the boulders(I am not indicating that Obito himself did it, unless well... I'll explain that in a moment), and move him to a place where things could be done to him.
The silly part of this, of course is that it wasn't in the same time as when Obito was crushed, but a different one, or even a place outside time. In other words, somebody used time hax, and time travel is actually involved to some degree. As to why it hasn't been abused to hell and back earlier... Well, in Kishi's defense, at least the plot hole in that would be nowhere as big as the "Tobi is Obito" bit by itself, and it truly shows that "Sharingan = Hax", something that I believe is implied, if not outright spelled out to everyone, during the course of this series.
I would love to know what people would think of this silly thought of mine, truthfully. And I do hope that Kishi does have a good explanation for all this. That is all.