Madara was suppose to be the 3rd Coffin [Plot Hole?]
I'm going to try to prove 2 things;
• 3rd Coffin must have been Madara
• Orochimaru was the one behind Madara's Mokuton (Little help from Kabuto)
Please understand this first;
You know that to do Edo Tensei you need to perform a ritual beforehand right? You need a living vessel and the DNA of the person you wish to bring back. Now imagine this scenario:
Orochimaru uses a living victim and sacrifices him, he calls on the DNA of Minato. Oddly enough Minato doesn't come back (Well because of the Shinigami Seal). Minato is then not revived.
So, after that how it possible for the 3rd Coffin to be Minato if the ritual wouldn't work beforehand?
As for Kabuto's chat with Obito, he was lying. If he told Obito "So yes he resurrected Madara", believe me, Obito would have killed Kabuto by seeing where he was going with this. He even lied about the hand seals to break it.
So he used Yondaime Hokage as a decoy.
Check this out first:
It seems Hiruzen somehow stopped the 3rd Coffin from resurrecting, NOT THE SHINIGAMI SEAL ON MINATO!
Despite what Kabuto said, he doesnt make sense, since what Hiruzen did here.
Concluding the 3rd Coffin must have been Madara
I think the fact alone that Madara was reanimated was proof Kabuto and Orochimaru had access to his DNA, what makes it more believable is this....
Now, Madara receiving Mokuton thanks to Orochimaru
How old is Yamato?
Kyuubi attack happened about 16 Years ago, and we all could agree Yamato got his Mokuton far earlier, since he got it since he was a kid, which btw Orochimaru gave him. I'm trying to say Orochimaru experimented with Mokuton even before Naruto or Sasuke existed.
Orochimaru really got skilled at manipulating Hashirama Cells well, he even granted Danzo Mokuton, though on a weaker bases. Danzo here was clearly the so to say "prototype" of what Orochimaru had in mind for Madara.
Here is little proof that Orochimaru or Kabuto did in fact give Madara Mokuton
Notice how he is checking out his wounds as if Obito should have done the "job" long ago (Whisper: He didn't want Madara involved...)
And finally the proof in the pudding;
"Damn Kabuto...not only was he able to reproduce the tree world...but the tree flower world!"
We can easily conclude Orochimaru/Kabuto did in fact experiment on Madara's body at some time.