You misunderstood what custom Pax Waypoints are for. They are ONLY used to customize a path passengers might eventually undertake AFTER the exist the jetway, for example to represent a fixed passenger bridge that is not part of the jetway object.
Everything happening "inside" the jetway is not customizable, because the jetway position is always different, so GSX use the waypoints from Jetway Navdata API. However, the height of the jetway "floor" is not something defined or standardized, so in order to fix this, you need to use the method explained at Page 71 of the manual, the chapter named "Custom Jetway Floor heights", which clearly explains the problem and how to deal with it.