Hi David, I just want to make sure I understand your exact issue so we can consider it in future requirements planning if we don't support it now. You'd like to modify the route with waypoints to force a user-specified route without having to treat that waypoint as a stop and click 'continue'.
Currently, you're correct that there is no way to set waypoints that aren't stops. ALN was originally built as a companion app to ArcLogistics Desktop so it was assumed all route editing would be done on the desktop and then pushed to the mobile navigator.