I know some people are thinking that Kishi broke conventions of preexisting story logic (again this time with how zetsu were created) but again, consider this:
According to black zetsu, white zetsu were created from people being in the IS long enough, this by all means could have happened in the distant past when Kagyua had the genjutsu up but it was stopped by unknown means. Most likely her sons stopped her.
What we were told before was that after his battle with hashirama, madara gained some of his DNA and years later managed to summon the gedo mazu from the moon. Because of hashirama's DNA, he was able to use this combined with the powers to the gedo mazu (it had a lotus flower chamber or so) he was able to use these to create an non-sentient clone of hashirama and as we have seen in the series, they possessed attributes to the wood style and as sakura discovered, hashirama's DNA. It was also because of the wood style remember, that like the shinju itself which could absorb chakra from anything, the senju wood style was capable of absorbing and suppressing tailed beast chakra.
So i think it comes out to this:
The Zetsu are created by means of artificial growth using DNA and the power of the gedo's lotus at least, or using humans as natural DNA source to convert them into white zetsu since like the latter, its all the same power but its greater since the shinju in this second case is fully restored.
The different types of zetsu (white, black, spiral) are the results of experimentation. White is the most common, spiral was otherwise as many guess, to have been madara's prototype. He did create black zetsu and for a time, yes black zetsu was actually his will. But because his will became influenced more and more by kagyua, eventually she was able to as many agree, manifest her will in black zetsu since black zetsu was by all means an extension of madara himself, think of it like this: Madara is himself, black zetsu is like a different clone of himself who always obeys. Because BZ was just a construct, not a real person, because kagyua resurfaced within madara when naruto hit him with the lava rasengan, she was able to emerge in him. This isnt the first time the will of one other has had another body to manifest themselves from, orochimaru did this through anko despite being sealed away by itachi.
So it still makes sense in that, yes black zetsu was made by madara, as were the rest. The presence of what can happen though to everyone in the genjutsu is that they literally will die because they wont even be themselves anymore.
It can be evenly assumed that madara (also maybe Obito himself) kept creating white zetsu for a time if the need for a great offense came (like the 4th war). The other is that, like kabuto, madara or obito could have covertly kidnapped many others around the world from time to time to create more. Maybe there were even leftover white zetsu from kagyua's time, so this could be a combination factor, with some leftover Madara was left to create others by means of just hashirama or covertly kidnapping others to form more white zetsu. Its because we know madara did make white zetsu, obito most likely joinied in. The fact of there having been 1000 year old zetsu waiting to be used, those created through Hashirama's DNA with the gedo lotus, and/or the same process of those trapped int he IS is occurring to make more but on a slower scale as what was happening right now are all viable. The last one may confuse you but it sort of could be say, while the shinju is doing its own work on them now, in this case before the shinju was made, perhaps kidnapped people were assimilated to the gedo lotus and this could have turned them into zetsu aside from the DNA growth one, remember yamato was assimlated to the gedo lotus but he lived because he was needed to empower the zetsu.
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alright picture that you have Sasuke's Rinnegan, you are on a field standing by one of two trees in the whole field and a ninja launches a Jutsu at you.......
