GraphUpdateScene shift-click in 2D and polygon collider

I’m using Unity’s 2D isometric tilemap currently on 2019.4 LTS, and I’d like to ask how to effectively use the shift-click option for the GraphUpdateScene in 2D view. It works when I shift to 3D view but once I use 2D it doesn’t work. But when I use it on 3D view, it is very awkward to use since it doesn’t accurately hit the 2D tilemap. As seen in the picture below, the point go below the tilemap even when I try to position the camera in the same position in 2D view.

Another thing is when I use the polygon 2D collider instead. I want to only add weights to certain parts of the graph. Since my tilemap is isometric, the polygon collider doesn’t perfectly follow the shape of the grid but instead uses the points of the square it creates. So instead of having my isometric grid having half weighted, it also hits the other nodes. Is there a way to fix this? Thanks!