Coordinates from mouse low level hook messages are not mapped the same way than WM_MOUSEMOVE or GetCursorPos. This causes problems on programs that make use of both values to calculate mouse movement, like the wine DirectInput implementation.
I'm marking this as a draft since I was not able to find a way to write a test for this. I'm able to easily reproduce it on Proton, because it creates a scaled full screen window, on Wine this doesn't happen so the coordinates are not required to be mapped to a scaled window.