I believe they originated from Susano'o depending the user. I mean Susano'o is literally holding these so called spirits, by that logic this should be impossible as well. We know Susano'o has phyical form and it can hold these weapons phyically as well, they've shown only with Susano'o and they look like the same material.
Like you said Madara being said the first Uchiha who had Susano'o, than we found out Indra who is ancestor of Uchiha has it as well. This shows some knowladge that we've been shared because of people are highly subjective. Around 100 years ago Hashirama did all that sh*t and before he actually showed those sh*t in ET form, people of the world considered them as Fairy Tale according to Kabuto.
So it is possible there were other Uchihas who awakened MS and Susano'o before and even used these weapons but after sometime people disregarded them as folk tales.
There very well may have been other unrecorded Uchiha with susanoo, but here is the thing, there was a lot of folktale in Naruto, and most of the folktale was never over exaggerated pertaining to the sage and his sons. The folktale of him creating the moon was true, the folktale of his sons waring against each other is true, the folktale of all his weapons & tools were true, the folktale about Kaguya and the God tree etc. is true. Most of this info was leaked through the lead investigators and analyst in Naruto (Orochimaru, Kabuto, Obito, Madara) the folktale revolving around Yata and Totsuka is vague, and they were present as treasures that could be found physically, unlike the folktale of Hashirama. I think If there were really other Uchiha wielding Sage tools through susanoo, that would have been part of the myth, but it wasn't, and seeing how the myths of the sage and his power that passed down through centuries turned out to be precise, I don't see any reason why it shouldn't have been.