from the docs
When you use set_cell, you can set the autotile_coord by setting all the parameters: set_cell ( int x, int y, int tile, bool flip_x=false, bool flip_y=false, bool transpose=false, Vector2 autotile_coord =Vector2( 0, 0 ) )
The vectors are set like you assigned in the tileset texture. If unsure, you can just save he tileset to a .tres file and open it in a text editor and look under [resource] > [number of the main tile of this autotile set]/autotile/bitmask_flags