### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
}
	} else if (shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		switch (bit) {
			case 1:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE;
				break;
			case 2:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_LEFT_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_CORNER)] = TileSet::CELL_NEIGHBOR_TOP_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE)] = TileSet::CELL_NEIGHBOR_RIGHT_CORNER;
				break;
			case 3:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE;
				break;
			default:
				ERR_FAIL_V(output);
		}
	} else {
		
		TileSet::TileOffsetAxis offset_axis = ts->get_tile_offset_axis();
		if (offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
			switch (bit) {
				case 1:
					output[base_cell_coords] = TileSet::CELL_NEIGHBOR_RIGHT_SIDE;
					output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_LEFT_SIDE;
					break;
				case 2: