@Thomas-Scharrer, I think you are referring to unplanned stops AWAY from the route? Yes, multiple recalculations in that case can throw off your route indeed. You can prevent that by adding the unplanned stop to your route on the fly (by long pressing on the map, or by the menu).
The track navigation will not auto skip waypoints like routes do. I think it will be a step forward in your case. Remember you can always re-enter the track at a desired location, simply by long pressing on the track where you want to re-enter.
But on the other hand, using routes you can also easily reroute through any desired shapingpoint by just pressing it...