I see where this is overengineered for the case of flying, but then flying navigation is a whole different game anyway. If you have waypoints, all you basically need is to add A* on top of it. In fact, your waypoint graph sounds alot like what I had in mind
And yes, this is what OpenBot did, but it used LavishNav so it's not really a good reference. And don't be fooled by the simplicity, I've built a 1-80 hands free bot on this simple scheme (though refined with some collision magic).
Nowadays, with all the public information and even code out there, and with RecastDetour, building a NavMesh is like a week of work. Hell, next week someone might just do the last and final step and release finished meshs for Detour.