So count all the instances were Kishi broke an absolute rule he set previously a.k.a. BS
Lets see how many we can remember(working my was backwards).
1. Spiral Zetsu using (lesser) 1000 Hand Buddha: he may be different to the other 10 000 zetsus but he is still a zetsu, neither is able to use any nature release jutsu. And if Spiral Zetsu was there all along then why didn't obito use him?
1) A ninja of high level can use more than one element. We've seen Sasuke use Fire and Lightning. We've seen Kakashi use water, earth and lightning. We've seen Hiruzen use all five. All it takes is training and ability to control chakra, and Spiral zetsu has had plenty of time to train.
2) Zetsu is a clone of Hashirama. Hashirama naturally had Earth and Water affinities (hence, wood). Zetsu may also have received some of Madara's "will", which would have fire affinity. After that, he only needs to learn two more.
3) Madara's body is part Hashirama/Zetsu. Zetsu can communicate telepathically through the ground. Therefore, Madara can communicate (and possibly pass chakra) to other Zetsus. Madara has Rinnegan, therefore any Zetsu borrowing his chakra can use it too
4) We know that the dragon- and Buddha-themed techniques in Hashirama's arsenal had the ability to absorb chakra. Spiral Zetsu is fighting shinobi of every nation, and therefore had opportunity to absorb chakra of all types
These are just four possible explanations for how he used those elements, I'm sure we could imagine more if we tried
2. Madara's Plug-n-Play eye: we saw Kakashi needed a medical nin to help with removing and implanting it, Sasuke was out for some days and had a blindfold, can't say anything about Obito's rinnegan.
And Madara has an enhanced body with Hashirama's cells and he has stolen much of Hashirama's chakra including senjutsu chakra. Hashirama has the ability to heal without using signs. In fact, we've already seen Madara heal his arm with that power. It's trivial to think he could heal his eye socket.
3. Madara's Susano'o: It is a dojutsu, it requires not one but two MS eyes, neither kakashi nor Obito have, both itachi's and sasuke's susano's vanished when they lost sight.
Tobirama explained that Sharingan had two parts: The sharingan itself and the changes that happen in the optic nerve and brain to activate the new power. Remember all that stuff about the older son of the great sage inheriting the sage's eyes and mind? Plus, Madara's eyes still existed and still worked, they just weren't attached to his head.
Admittedly, Madara using Susanoo without his eyes is a little bit of a hack, but it's not completely unreasonable.
4. Sasuke having PS: after getting EMS he spontaneously manifests Complete Susano'o... and then minutes later manifests PS after only hearing about it.
Sasuke hasn't used Perfect Susanoo yet.
5. Minato having KCM: died a minute after sealing Kurama and was running 10min(assuming) after getting revived so had no time to train plus the time he was sealed doesn't count since neither Hashi nor Tobi knew who he was yet they were sealed together
The Yin Kyuubi was sealed inside minato. Minato was sealed inside the belly of the shinigami for several decades. Minato has had plenty of time to train. ALSO, Minato was an expert at seals and knew many details about the Kyuubi and Bijuu that Naruto never knew. It's not impossible to think that he could pull this off.
