I do not present this as an expert opinion, but just based on observations over a span of many years. Oak has tannic acid. In the presence of moisture, this acid turns steel black and stains the wood. Some other species of wood do the same thing. These stains are difficult to eliminate. Even the metallic content of sanding dust will stain oak if the dust gets wet while on the wood. Sanding is frequently done with aluminum oxide, so metals other than steel may also stain woods. I suppose that you really wish to be rid of the black dots. Obviously, replacing the floor or covering it with something else are two of the options. Dark staining the entire floor will help lessen the effect of the stains. I have no other suggestions at the moment.

It has been my experience that if a really good match---like with the Stain Putty---is not possible---like trying the color sticks/sawdust and glue/---making the filler lighter is less eye catching. I did several hundred feet of pine crown molding, stained dark walnut. The home owner specificially mentioned he wanted no conditioner---he wanted the color differences from the stain to show. And with even good stain grade pine, there was a LOT of difference. It was in a room with 7' ceilings and a soffit for HVAC in the center the length of the room that was 10" below the ceiling. I used a 16 gauge nailer and had a lot of nail holes to fill. I made up two batches of Stain Putty----one with the dark walnut stain and another with pecan stain. The dark walnut Stain Putty was a perfect match for the darker areas---but would have stood out like a sore thumb on the lighter areas. The pecan was a bit lighter than the light areas and was a fdair match---the HO could not see the filled holes----and he is a professional painter---has owned his own company for 30 years.

I just looked up water popping, since I was unfamiliar with it, and apparently its VERY tricky to get it right various causes of blotchiness include uneven application of the water, wood not evenly or completely dry before staining, etc. Im no pro,...just someone who's futzed around with wood for a long time. In some spots it looks like it might have to do with the grain of the wood and how its absorbing the stain. I might be willing to accept the blotchiness as just quirks of the wood.... maybe.... but not the swirl marks - that's just amateur. My sympathies, such beautifully grained wood deserves better!

Expansion gaps is different from using adhesives as a fastener. I was skeptical about the product working at first, also. But if, you are using the correct type of adhesive (Silane based polymer) for solid wood. The flooring will be able to expand and contract as needed. The adhesive never hardens. Polyurethane adhesives are brittle, after it is cured. Not recommended for solid wood flooring. The conditions do have to meet the adhesive mfg's guidelines, though.