The draw route function is a computer algorithm, not a pre-researched path by a human being (me). It starts off at the western-most node and find the nearest closest node and connects to that, and it keeps connecting to the nearest nodes until there are none left, which may not give the ultimate shortest path because of backtracking to farther away nodes, but it should be good enough on average.
The waypoint or chatcode generation algorithm reads the finished connection, and for each node, it finds the nearest waypoint, which may be behind a wall or a cliff that you have to walk very far across compared to a rivaling nearest waypoint.
The solution to this is for me to manually record the nearest proper
waypoint into the node itself, rather than by algorithm. Of course, I'm only willing to do this for permanent nodes, and I can't promise how soon I'll add it.
You say that you frequently farm nodes, so I suggest you copy and paste the chatlinks into the notepad app
and correct it with the waypoints you want.
Edit: I forgot about the save pins function. You can customize the route by dragging a pin to the waypoint you want, then right click on the map: Pins > Save. Then when you want to view the waypoints: Pins > Load, Pins > Chatlink