https://www.wired.com/story/book-excerpt-science-of-ultra-pure-silicon/

As I said, we can make nine 9 silicon. But not eleven 9. China makes billions of nine 9 silicon chips per year. But they can’t make eleven 9. Everyone is trying to create lab made eleven 9, it might not be possible. The natural stuff formed over hundreds of millions of years with basically no exposure to water. Which means no contaminates.

So yeah, we’ve not succeeded in recreating that.

That's not what is in the article you linked.

The very best Spruce Pine quartz, however, has an open crystalline structure, which means that hydrofluoric acid can be injected right into the crystal molecules to dissolve any lingering traces of feldspar or iron, taking the purity up another notch. Technicians take it one step further by reacting the quartz with chlorine or hydrochloric acid at high temperatures, then putting it through one or two more trade‑secret steps of physical and chemical processing.

The result is what Unimin markets as Iota quartz, the industry standard of purity. The basic Iota quartz is 99.998 percent pure SiO2. It is used to make things like halogen lamps and photovoltaic cells, but it’s not good enough to make those crucibles in which polysilicon is melted. For that you need Iota 6, or the tip‑top of the line, Iota 8, which clocks in at 99.9992 percent purity—meaning for every one billion molecules of SiO , there are only 80 molecules of impurities. Iota 8 sells for up to $10,000 a ton. Regular construction sand, at the other end of the sand scale, can be had for a few dollars per ton.

You wrote

The natural stuff formed over hundreds of millions of years with basically no exposure to water. Which means no contaminates.

From the article:

It took some 100 million years for the deeply buried molten rock to cool down and crystallize. Thanks to the depth at which it was buried and to the lack of water where all this was happening, the pegmatites formed almost without impurities. Generally speaking, the pegmatites are about 65 percent feldspar, 25 percent quartz, 8 percent mica, and the rest traces of other minerals.

The quartz they produce has a structure that makes it easier to clean so, when making the quartz crucibles for manufacturing silicon wafers it is the best choice. But the purity isn't eleven 9s, the highest quality is 99.9992% purity.

Silicon wafers are made out of even more pure silicon (9n), which is melted in the nearly pure quartz crucibles. The Spruce Pine quartz is for making the crucibles, not making the wafers.