Is because there are no nodes on the gridmap, is just like a node with a bunch of meshes.
Transform the Node position to gridmap coordinates (Tilemap has a method for that but gridmap not), should be like "translation/grid size" rounded down.
With that position you can get the cell item below it (y-1), knowing the cell item you will see if exists (!=-1) and if can be removed/changed according the cell item data, to remove it just set the cell item as -1, like with Tilemaps.
I think there are requests for updates on Gridmap (which lack of a lot of features comparing to Tilemap), you can search and support these requests on GitHub to give it more attention for contributors (or add features yourself if you can).