In the Garmin they have two different types of waypoints. Waypoints and shaping points. The shaping points help to create guidance that uses particular roadways. So once you pass over them or past them on your travel they go away automatically. Basically if the navigation device recognizes that you are in a position further along in your custom route, it will automatically skip any shaping points you have passed, and will continue navigating to upcoming waypoints or other shaping points. Waypoints, however, you have to manually skip.
This is a functionality I'm looking for in a navigation app for my phone.
I just wanted to comment that I used the Skip Waypoint functionality the other day. But the problem with it was that when it goes to that mode the buttons and text get rather small and harder to hit while on the bike. I would love to see those buttons come up sized better for being on the bike doing this. Just some bigger buttons with larger text like the buttons on the slide out when you hit the 3 dots.
Still not an optimal solution like a shaping waypoint, but its a step forward.