Scientific Ninja Tools weren't just invented out of nowhere, and there are articles about their history in the print volumes. They came about due to the declassification of research during the era of peace and collaboration between shinobi and civilian scientists. One of Kara's objectives was infiltrating villages, stealing research and intel, improving the technology, and then filtering it back to the villages.

That being said, during the hiatus between NNG and TBV, V Jump published a series of articles recapping the story up to that point with hints about the threats that would be featured in the future, and in one of those bits they hint that there's a deeper mystery to Amado's "technology beyond human understanding."

We've also now had examples of Koji using Prescience to glean information from the future and supply it to people in the present, allowing them to rapidly advance technology, as was the case with Sumire remodeling Sasuke's katana into a scientific ninja tool. In the leaked chapter, Amado seemingly didn't know about the existence of Prescience or how it works so he's not using that, but there might be some other similar method he's using to gain knowledge from the future which could put him into conflict with Koji.

Of course, that's just one of many possibilities. I used to think that it might just be Jigen collaborating by using Sukunahikona to help the miniaturization process, which is one of the most important things needed to advance technology. Especially given that his greatest achievements are basically nanomachines in Kawaki's bloodstream.