I can see why a company would like you to use their own measuring device to do performance testing. Wow this car can do 400mph according to the speedometer!
But seriously, with iPerf I am usually interested in finding the cause for performance issues (usually detecting the worst cases). If that is a bad emulation layer in Windows, that is what I am expecting to find. If MS would like all applications to use some other OS-calls or libraries or complete tool chains, they should make them easily available, portable and compatible. If this has been arranged already, it should not be any problem for MS to just create a pull request for iPerf3 and fix the problem.
This would also fix the problem with all the other applications that are using the same network libraries. I would assume MS have fixed a native version of Git by now, that is not relying on MinGW. But I am sure a lot of other software still do. So for these iPerf3 will tell the truth. While ctsTraffic etc. will give you some theoretical number.