When madara or the sage of six paths explained kayuga's story it just seemed like the tree was there to strong-arm people into worshiping her. The only thing is zetsu is the only person never given any back story. As far as someone calling this, I think it did happen WAAY early in the shippuden when someone remarked on Zetsu's mysteriousness and the lack of explanation of his abilities. I think it was when someone said he was weak but could teleport/transport himself anywhere without anyone noticing. That theory was quickly tossed to the wind when he was absent from like every fight. Then he became a "fodder" villain when he was mass produced for the zombie army.
All in all the events in this manga range from being too farfetched then ringing true, to being sound and being found nowhere in the plot at all.