[mort96]

I got results with a P-value of under 0.001. That should be enough to demonstrate that there's a real difference.

Using a camera allows the methodology to he identical between Wayland and X, while I don't know how to listen for mouse movements from software in a way that wouldn't introduce its own problems. What if the photons are emitted from the screen after the same number of milliseconds across X and Wayland, but Mutter is a few milliseconds slower about notifying my measurement application? Conversely, what if Mutter has more real latency than X, but the latency is introduced after the stage where my measurement application sits?

The variables you mention are identical between the Wayland test and the X test. It is admittedly a challenge for reproducibility, but doesn't affect these results.