I don't know anything about the wayland API. Does this imply that windows can't have a different scaling on each screen they may overlap on? Or can a window be split across different surfaces?
Wayland surfaces (windows) have integer property, that says at what scale they are rendered. Compositor then suitably scales them for target displays. If a surface is at two different displays at two different resolutions, it will be scaled correctly on both (up or down; depending on the application; in practice downscaled on the lower resolution one).