You are wrong. The IAAF rule in place in 2016 did not mention prototypes. You are thinking of one of the many revisions of Rule 143 that happened in the fallout of the Vaporflys. Here is text of IAAF Rule 143 as of 2016:
So are you arguing that the 2016 prototypes were not constructed to give athletes unfair assistance or advantage and were reasonably available to all? You admit yourself that they turned out to be way better than any before. Those Vaporfly prototypes were the first racing shoes to actually provide a step change improvement in performance. And the technology ("type of shoe") definitely was not reasonably available to all, where other brands having shoes of similar technology and performance could be considered reasonably available to all.
Oh, and you can't just say Nike made the first shoes that just happened to be, somehow unknowingly by Nike, way better, as you say. They had the data on it. They just didn't release the data showing how good the technoloogy was until March 2017, well after the 2016 US Olympic Trials and the 2016 Olympics. By then the cat was out of the bag, too many people had been using them before the IAAF could react, just like the Uber analogy I made in the first post. IAAF had no choice but to have to change Rule 143, and they've revised it several times since then.
FYI the analogy isn't correct. Uber wasn't "breaking taxi laws". What happened was that pre-uber, there were two classes of car services essentially: Taxis (flagged down and not needing to be prescheduled) and car services (needing to be prescheduled). Taxis were much more heavily regulated, while car services were not, and essentially just couldn't "operate as a taxi" ie have random passengers flag them down off the street.
What uber did was regulatory arbitrage by allowing passengers and drivers to more easily "preschedule" rides via an app, rather than needing to call/schedule further in advance or two/from specific places. This was definitely a bit of a grey area since the rules in many cities essentially allowed a "prescheduled ride" to be only moments in advance of the pickup (again, unlike a taxi which is flagged down).
I am oversimplifying, but Uber was not "breaking taxi laws" because Uber wasn't a taxi service (which was a specific class of service). It was a way to more conveniently schedule "prescheduled" rides, which resulted in the old Taxi model becoming somewhat obsolete. Should prescheduled rides have had more regulations pre-Uber? Maybe, but that was the fault of cities for focusing only on Taxis, not the fault of Uber breaking laws that didn't apply to them.
Also old taxi laws and medallion systems were horrible for consumers (and taxi drivers) and people vastly prefer modern ridesharing services.