So it seems I can add a variable inside <project>/Config/DefaultEngine.ini
:
[ConsoleVariables]
Slate.Transform.FullscreenMouseInput=False
This fixes the problem!
But also, this variable is true by default, and given this description:
"Set true to transform mouse input to account for viewport stretching at fullscreen resolutions not natively supported by the monitor."
So it may be a non-solution. But whatever the case, I still think this is an engine bug. At least the text description should be changed to "[...] not natively supported by the primary monitor."