UP!, I have the same problem. One little difference is that I'm using autotile with navigation mode, and thus, as far as I understand, I should join all the tile polygons into a bigger one in order to use clip_polygons, and this seems too complicated to be the solution (I tried in fact, but failed miserably).
Idealy, I want to carve holes in the navigation mesh as borders of a procedural generated map (The map is bigger than the game area)
Please share here if you find a solution.