Yeah I agree with you. It does seem far fetched, I also said the same several times, when I heard it. How would anyone suddenly know how to use it? Unless Gaara somehow just gets a flashback of seeing it in use. I mean it's Kishi, he can do whatever he wants. Heck even Minato for that matter...
But sadly Kishi doesn't just have Madara spit those tools out for no reason... it was a bit funny btw, that they hit Gai and Lee! (thumbs up Kishi)
And there is one, who could potentially know how to use them, without being some plot joke, that is Obito.
Lets put up a scenario:
Gai and co. arrives before (or even after) Madara fodderise Gaara, Kakashi and Minato and takes his last eye. Gai uses 8th gate, which could potentially make him capable of stalling Madara for a while. I doubt even Madara knows anything about the type of "techniques" one can use, when using the gates. This would give Gai a huge advantage, and thus it would not be plot haxed, if he was able to surprise Madara and thus delay him from taking his last eye (or even fight him with his last eye, if he already took it).
Now this gives the possibility for either Kakashi and co. beating black zetsu and brining Obito back. If they have already been beaten, there is still Lee and TenTen, though they wouldn't know sh*t, would they? It would require Gaara or someone else to tell them, what to do.
Lets say Black Zetsu starts by giving Madara the Kuybi, which makes sense, so that the sage tools will have to be used to save Naruto. Then they could bring down black zetsu, and thus bring back Obito. He could at least do something to fight Madara as well, and he could possibly use the tools or tell someone how to use them.
And we must assume Sakura has no part in all this, as she needs to keep Naruto alive. Then it could make sense...
I don't think Naruto lost the gifted chakra. It was just the Kuybi Madara pulled out of him. I doubt he went for anything else, and he wouldn't even know it. Obito didn't realise it either. Seems only Bee and Naruto know it.
Btw regarding the mystery man, would it not be so like Kishi, if that is actually Yamato who suddenly mastered mokuton senjutsu

just to freak everyone out about who is inside spiral zetsu