### 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)
tile_lines_mesh->add_surface_from_arrays(Mesh::PRIMITIVE_LINE_STRIP, a, Array(), Dictionary(), Mesh::ARRAY_FLAG_USE_2D_VERTICES);
		tile_meshes_dirty = false;
	}
	if (p_filled) {
		p_canvas_item->draw_mesh(tile_filled_mesh, p_texture, p_transform, p_color);
	} else {
		p_canvas_item->draw_mesh(tile_lines_mesh, Ref<Texture2D>(), p_transform, p_color);
	}
}
Vector<Point2> TileSet::get_terrain_polygon(int p_terrain_set) {
	if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
		return _get_square_terrain_polygon(tile_size);
	} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		return _get_isometric_terrain_polygon(tile_size);
	} else {
		float overlap = 0.0;
		switch (tile_shape) {
			case TileSet::TILE_SHAPE_HEXAGON:
				overlap = 0.25;
				break;
			case TileSet::TILE_SHAPE_HALF_OFFSET_SQUARE:
				overlap = 0.0;
				break;
			default:
				break;
		}
		return _get_half_offset_terrain_polygon(tile_size, overlap, tile_offset_axis);
	}
}
Vector<Point2> TileSet::get_terrain_peering_bit_polygon(int p_terrain_set, TileSet::CellNeighbor p_bit) {