The answer is to make the changes in the RoutePlanner not in MRA Navigation.
This should keep them both in sync.
Controversial posts made by Steve Lynch
RE: MRA Navigation (Android): Edits on Route Editor not synced to MRA Route Lab (web)?
RE: Differences between MyRoute-app and the Navigation app
Inserting a couple more waypoints between 2 and 3 in the first screenshot would probably fix that in Navigation.