Your issue here would be that the way prices are calculated changed as well. The business models are not the same. In the 90s all board manufacturers charged a fixed setup fee, which did not depend on the board size (apart from extreme cases). Then first articles would be produced at a high markup again. But after that the same set of masks could be used for mass production, which is relatively cheap. The setup was not affordable for modern understanding of "prototyping". And for mass production, where setup cost is amortized, the prices have not changed that drastically.
Direct imaging, high levels of automation and overall improvements in the equipment enabled cheap setup, which gets absorbed into the cost per inch for low quantity orders. Plus in many cases those $10 prototyping offers are loss leaders, they don't make any money on them. This was not a thing in the 90s at all.