There is no debate. All of them intentionally display higher than the actual speed. The only thing I don't know, which someone else is sure to, is whether the ABS and non-ABS models behave the same.
Mine is a non-ABS model. The speedometer reads several percent high based on stock sprocket ratio and tire sizes, and since the speedometer signal is based on an output-shaft speed sensor inside the transmission, it will be wrong by a further factor if you are using a non-stock final drive ratio or tire sizes, since it has no way to know the difference.
The thing that I don't know, is whether the ABS models behave the same way. Those have actual wheel speed sensors front and rear. Lots of modern vehicles get the vehicle speed for the speedometer from the wheel speed sensors. I have no idea if Yamaha has done this. The output-shaft speed sensor is still there, so it could be done either way. On an ABS model if the speedometer keeps the same designed-in error factor if you change sprocket ratios, then they're using wheel speed sensors. If it gets messed up the same way then they left it with the transmission output shaft speed sensor.
For the ABS-equipped models, it wouldn't surprise me one bit if the 2018-and-before models behave one way and the 2019-on models behave another.
I have a 2020 w/ABS and it's surprisingly spot-on accurate. I'm using the WAZE app which pulls GPS on a Pixel 4XL. Higher speed can lend to more deviation if it's off, so I'm still in break-in (30 miles to go) so top speed is 70 mph. At 70 mph it reads 70 mph sustained.
It's a known fact most speedos are 10% or so higher reading, Honda being the biggest culprit over the years in the past, sometimes reading 12% off, but this is intentional.
Different tires will change this value a little, as well as changing either sprocket up or down a tooth (or two). I switched to Battlax RS-10 tires but there was no change. I suspect Pirelli tires which are generally taller might throw this off a bit. I remember my Ninja 250R with the MT10 Pirellis would be off 5% slower than before (so more accurate because the 250 was reading 7% higher normally).
I suspect the new-generation electronics (2019-on) are using the wheel speed sensors for the speedometer. If changing the sprockets doesn't screw up the speedo (relative to GPS or "your speed" signs) then for sure it's using the wheel speed sensors.
Everyone seems to be assuming that GPS speed readout is accurate but this is not alway true. Most of my GPS units display "GPS accuracies" and it varies from time to time. I was touring on my 99 VFR800 two up and loaded and the GPS max speed showed 156 mph.