@Steven-Farmwald A route is just a list of waypoints (GPS coordinates). It is up to each application or device to figure out how to actually get from each point to the next. This depends on its map and algorithm (e.g. Google uses a different map and algorithm than HERE to calculate routes. Note that the Google map overlay in MRA is just that: an overlay. MRA doesn't use Google to actually calculate the route, it uses either OSM, HERE or TomTom). So there is no guarantee that an exported route matches what you planned to begin with. The waypoints will be in the same place, but what the route between those points looks like, is up to the importing application or device.
In addition, MRA provides a feature to "skip" a waypoint (which effectively means route calculation is disabled to that point, i.e. you get a straight line from the previous point). However, this information is not stored when saving the route as GPX or KML (because the GPX and KML file formats don't include that information), so other applications don't know about skipped waypoints at all.
The fact that the other ferries are "correct" doesn't mean the points are skipped, it just means that Google Maps thinks that's the best/fastest way to get to the next point.