### 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)
for (const TileMapCell &E : edited) {
			Vector2i coords = E.get_atlas_coords();
			Rect2i texture_region = p_tile_set_atlas_source->get_tile_texture_region(coords);
			Vector2i position = texture_region.get_center() + p_tile_set_atlas_source->get_tile_data(coords, 0)->get_texture_origin();
			Vector<Vector2> polygon = tile_set->get_terrain_polygon(terrain_set);
			for (int j = 0; j < polygon.size(); j++) {
				polygon.write[j] += position;
			}
			if (!Geometry2D::intersect_polygons(polygon, mouse_pos_rect_polygon).is_empty()) {
				
				p_canvas_item->draw_polygon(polygon, color);
			}
			for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
				TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
				if (tile_set->is_valid_terrain_peering_bit(terrain_set, bit)) {
					polygon = tile_set->get_terrain_peering_bit_polygon(terrain_set, bit);
					for (int j = 0; j < polygon.size(); j++) {
						polygon.write[j] += position;
					}
					if (!Geometry2D::intersect_polygons(polygon, mouse_pos_rect_polygon).is_empty()) {
						
						p_canvas_item->draw_polygon(polygon, color);
					}
				}
			}
		}
		p_canvas_item->draw_set_transform_matrix(Transform2D());
	}
}
void TileDataTerrainsEditor::forward_draw_over_alternatives(TileAtlasView *p_tile_atlas_view, TileSetAtlasSource *p_tile_set_atlas_source, CanvasItem *p_canvas_item, Transform2D p_transform) {