This is an incredible writeup. I've visited almost all of these sites to inspect the masonry, spent weeks researching, pestered tour guides and museum workers for oral history, and still I learned things in reading this article.
However there is one aspect which I think is incomplete. When you closely inspect the seams of some of the non-layered works like sacsayhuaman, we are talking about 2mm precision along curved, inconsistent lines of two stones. The when you look at the joints up close, they make the joint between flat cinder-blocks look chunky.
The author posits that this was all hand chiseling and eyeballing, or scribe tools. However I believe there would be occasional gaps or inconsistencies, which simply aren't present in any of the pre-colonial precise works.
One thing I discovered in my research of other central American indigenous cultures (inca was a melting pot of culture and technology) was the use of rope or string, sand, and water to finely cut stones and gems. It is pulled like a circular sand paper and I believe this process would have been used, run between both stones being joined at once, in order to achieve the final tolerances through uniformly wearing the proud aspects of the joint on both sides.
> the use of rope or string, sand, and water to finely cut stones and gems
I haven't heard this one before, that's a great idea. Here's a YouTube video of somebody doing this with jade if anybody is curious:
https://m.youtube.com/watch?v=w_9MCNgY2Ww