> What happens - either in X or Wayland - if one window spans displays which are not in the same orientation?
One kind of rendering would be used.
Wayland has no notion of displays, really. An application just gets a surface to paint on, which might or might not span several displays. In case of multi-display surface Wayland can use 'unknown' subpixel ordering.
> And as an aside, I still think subpixel font rendering is a totally stupid idea, in part because of this very issue which means that the font renderer needs to have precise knowledge about the specific output device at any time
Uhm. It has this knowledge in 99% of cases. And personally I prefer occasionally looking at blurred screenshots rather than looking at blurred text _all_ the time.