Here's my take:
If a study comes out with: Brand X is far the best brand. All their shoes are ahead of the best of the rest.., then Brand X paid for the study and created results to their satisfaction. I am suspicious of the conclusion unless a bunch of other studies show very close to the same. There are a number of ways this can be done without any outrageous lying.
Take a bunch of Nike-sponsored runners. They can be B-list; doesn't need to be Kipchoge but could be. Even if you do remove logos/spray paint black/whatever, they will recognize the shape and style ummediately when the shoes familiar to them are next up. They may think, perhaps only subconsciously, 'these are the good ones'. A placebo effect can create measurable results. Even if you successfully obscured the look of the shoes (hard to do for models the particular runner regularly uses) you're starting with runners who know how to run in a particular shoe. It is often said that certain models require certain form to be most effective. Runners with certain small nuances in form already ingrained will run better in the shoe in which those movements became natural than something else objectively equivalent.
Other methods to sway results in favor of your intended outcome may include: The order in which the shoes are tested. You have been noticing during mile repeats on a treadmill that the 3rd rep is often the physiological high-point for the average athlete. Fewer, you're less warmed up; more, you're more fatigued. So, put the AF (for those who usually race in it) in for #3: the VF (for it's fan club) on the same rep. Test the other Nikr on #4. Put asics (or whatever you're most concerned about beating the system) in last. The actual equipment hooked up to the runners honestly WILL show results that suggest Nike is the best. You can (sort of, almost) honestly claim you didn't have your thumb on the data scale.
You can also simply leave significant competitors out of the line-up. The study mentioned by the OP didn't test anything from adidas. Where does the 3rd version of their flagship marathon shoe stack up? What about the Takumi Sen (lighter than all more heavily cushioned marathoners of any brand). You can even get the brand new, not really available to the public, model from your preffered brand but an older model from your competitors. This could be done accidentally simply because your sponsoring company gives you their best but you couldn't buy the latest from the others. For example, it seems extremely likely that Hoka's completely revamped Rocket X 2 would outperform the original Rocket X. No problem there, we'll just test the old one.
Here are the results that I trust:
The tests were done at a non-Nike-affiliated university or lab. Not BYU, not CU, not UCLA, etc. The runners were a wide variety of body sizes (tall and short) and even ages (so that you're getting some who went to HS before Nike completely dominated the HS scene and therefore don't view them as a 'starting point'). Find very good runners without a shoe sponsor and without a school sponsor. Find some, perhaps masters, who are good - well under 3 hours - but perhaps not genetically in the top 1%. Get the results.
Then, several other universities or organizations find similar results. By this time, hundreds of runners - a real wide variety - have been on the treadmill. PhD candidate testers who seek respectable thesis data have tried all combinations of different orders of shoes, temperatures and humidity, shoes painted different colors (to see if purple subconsciously feels faster to some), everything....
If results from 10 different studies show similar results....THEN I trust and believe the data. A single study done in Beaverton? I do not.