I think you're right about “dark matter,” and precision machining is exactly the first example of it that leapt to mind. E.g., Watt was having a hard time getting his improved steam engine to work reliably, because without a very good fit between the piston and cylinder, steam pressure would be lost. The problem was solved by Wilkinson, who had developed a special technique for boring canons that could be applied to cylinders for engines. This story is told toward the beginning of Simon Winchester's book The Perfectionists (sold in the UK under the title Exactly, I think).

I gave a related example about the non-obvious importance of precision manufacturing in my essay “Why did we wait so long for the threshing machine?”

Another one that comes to mind is chemical synthesis. Think about how much in the chemical and pharmaceutical industries relies on our ability to synthesize chemicals. And yet, this is rarely discussed even in books on the history of technology. Every once in a while I marvel that we can just synthesize molecules. How do we do that? And how did we learn to do that?!

Or, consider the semiconductor industry. To even invent, say, the transistor, we needed the ability to make n-type and p-type silicon. I haven't dug into it yet, but it must have required sophisticated materials processes to perform the appropriate doping of boron and phosphorus, which are present in the silicon in minute quantities.

One more: When I looked into the history of smallpox vaccines, I found that there was a lot of iteration after the initial vaccine to improve safety, storability, and transportability:

Small amounts of vaccine could be stored for a short time on ivory points, between glass plates, on dried threads, or in small vials. But the virus would lose its effectiveness quickly, especially when subject to heat. When King Charles VI of Spain sent a vaccination expedition to the Americas as a philanthropic effort in 1803, the crew took 22 orphan boys: one was vaccinated before they left, and when his pustule formed, a second boy was vaccinated from the first, arm-to-arm; and so on in a human-virus chain that sustained the vaccine during their months-long voyage across the Atlantic.

Degradation, especially from heat, is a general problem affecting organic material. There are two basic solutions: refrigerating (or freezing), and drying. Before refrigeration, or when it was expensive or otherwise impractical, such as in tropical regions during the World Wars, drying was necessary. The challenge is that the simplest way to dry a material is to heat it, and heat is what we’re trying to protect the material from. Further, drying would often cause proteins to coagulate, making it difficult to reconstitute the material.

The solution, developed in the early 1900s, was “freeze drying”. This technique involves rapidly freezing the material, then putting it under a vacuum so the ice “sublimates”: that is, water vapor evaporates directly off the ice without ever melting into water. A secondary drying process (involving mild heat and/or a chemical desiccant) removes the remaining moisture, and the result is dry material that has not been damaged in structure. If properly sealed off from moisture in the air, the material will last for a long time, even when subject to heat, and it can easily be reconstituted by adding water. Freeze-drying was first applied to blood transfusions in the 1930s; Leslie Collier, in 1955, found that it allowed the smallpox vaccine to last several months even at 37° C (98.6° F), which was suitable for tropical climates.

Think about all of the underlying technologies that are required to invent and scale up something like freeze drying. Progress is highly interconnected; it compounds.

Re: other examples - true interchangeable parts, which was a major manufacturing advance, required a lot of advances in precision manufacturing. It had been attempted as early as the early 1700s, and was made much more feasible/cost effective by the invention of high-speed tool steel in the late 1800s, which made it possible to machine heat-treated parts. Interchangeable parts was, among other things, one of the technologies that made Ford's assembly line possible (iirc, Ford was the very first car manufacturer to use interchangeable parts.) But as late as the 1940s, it was still expensive to get true interchangeability, and wasn't always used.

I've looked mostly at progress from an energy lens, and I think the upper bound constraint for progress is relevant there too. 

Coal was restricted largely to space heating until the steam engine, which itself was restricted to stationary applications until the steam locomotive. Oil's first beachhead was kerosene lamps, decades before internal combustion engines were commercialized. Electricity needed the build out of vast, centralized grids and large coal and hydro power stations. I wrote more about this in this section of a recent long read.

I'm also very interested in the question of how to best accelerate the "dark matter" ecosystem and fast track the next AlexNet in whatever domain it happens to be. I too would be interested to see examples of domains that require minimal infrastructure and dark matter. 

For example, what could be done to make the AlexNet happen 10 years earlier?

I know it might be a heretical question on this forum, but do we really need to accelerate AI? Isn't there some point at which we can say "fast enough"? Like if we could press a button a make AGI appear today, would be wise to press that button? Are we truly ready for the consequences of what would arguably be the most important moment in our entire history? Aren't there enough other things in society that we could fix instead?