I’ve never done this orientation, but can’t you just pull the app window by clicking the top app bar? You just pull it away then move it back to the top of the screen to activate the auto window sizing/dock thingie and then it’ll just resize to the space? Might not work and it should’ve corrected when OP changed to this setting in the first place, but there’s always manual resizing of the application window too (though obviously annoying).