Ciao Bart, this morning I tried with my smartphone, following a short track near my house using 2 favorites points and I got the messages...
I transformed them in waypoints, delete the favorites and navigate again but I didn't have any messages... I added a favorite and the message come back again...
Clicking on the 3 small points next to the favorite name you can set the distance when the message start.
So at this point "intermediate points" are not considered neither as favorite/POI nor as real Waypoints (the main points the engine use to calculate routing, distances etc..). They are just icons connected to the track.
Another good option I discovered is that, in Directions, when you follow a track, if you press on the opposite arrows that you normally use to invert start/finish point, osmand engine invert the calculated route, you start from the end of the track to reach the start.
This can be very useful for tracks that have the same itinerary way there and way back.