I'm pretty sure this is incorrect? I half-remember having cursor rendering bugs on GNOME Wayland with NVidia ages ago which I had to disable something h hardware cursor related to fix. But I don't know if that's what you're talking about or not. Could you link to a source which says that Mutter doesn't make use of hardware cursor?
(Hi, author here by the way! ... Don't worry, that disabling hardware cursors thing was at least one OS re-install ago)
Yes, it should use hardware cursor by default on most hardware. But I don't think that RPi's VideoCore (in the linked article) supports hardware cursor or multiple planes. The difference between X11 and Wayland might then be that the cursor isn't vsynced as part of the composite process on X11, where it is on Wayland.
Mutter definitely throttles cursor updates on Wayland, too, which will contribute slightly to latency even with a hardware cursor. In general, with Wayland, the compositor is responsible for cursor updates, and I'm not sure which other ones throttle. But that would be where the difference comes from when using hardware cursors.
I think the difference mort96 is seeing is the cursor update throttling. If it updates at the same rate of the refresh rate then it's a crapshoot where in that interval it hits relative to vsync, with a worst case additional latency of the frame rate. X11 updates the cursor whenever it moves, so on scanout it's always where you expect it to be, even if the motion was almost immediately before vsync.
I should mention that in the past there's been problematic interactions on amdgpu with atomic updates of the cursor and display planes. This resulted in either one being starved from changing, causing stuttering in one or the other depending how it was handled. IIRC, that's why the throttle is there. You could try MUTTER_DEBUG_ENABLE_ATOMIC_KMS=0 to see if they only added the throttle to the atomic code path.
I wonder if the latency is due to the compositor receiving a damage event for the area of the cursor, thus being a frame late to render. But probably that wouldn't be an issue with hardware cursors.