Yay! Configurable origin and axis direction has landed, courtesy by @RRPollack. See User-selected PCBnew display origin (5.1.x) for background, but that thread is closed. (Please no bug reports or wishes here.) The feature won’t be integrated into 5.1.
EDIT: I wrote a FAQ article about the origins and coordinate system, Coordinate system, grid and origins in Pcbnew (especially version 5.99). It shows these new features.