I have a fix now that I’m satisfied with, see https://bugzilla.libsdl.org/show_bug.cgi?id=3931#c18
In short, I check the windows version (once, saved in a static variable) and if it’s Win10 FCU or newer, a workaround is enabled.
The workaround just generates an additional mouse event with the coordinates of the center of the window whenever a windows WM_MOUSEMOVE event comes in (if warped relative mode is enabled).