### 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)
ps->body_set_collision_layer(body, physics_layer);
						ps->body_set_collision_mask(body, physics_mask);
						ps->body_set_pickable(body, false);
						ps->body_set_state(body, PhysicsServer2D::BODY_STATE_LINEAR_VELOCITY, tile_data->get_constant_linear_velocity(tile_set_physics_layer));
						ps->body_set_state(body, PhysicsServer2D::BODY_STATE_ANGULAR_VELOCITY, tile_data->get_constant_angular_velocity(tile_set_physics_layer));
						if (!physics_material.is_valid()) {
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_BOUNCE, 0);
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_FRICTION, 1);
						} else {
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_BOUNCE, physics_material->computed_bounce());
							ps->body_set_param(body, PhysicsServer2D::BODY_PARAM_FRICTION, physics_material->computed_friction());
						}
						
						ps->body_clear_shapes(body);
						
						int body_shape_index = 0;
						for (int polygon_index = 0; polygon_index < tile_data->get_collision_polygons_count(tile_set_physics_layer); polygon_index++) {
							
							bool one_way_collision = tile_data->is_collision_polygon_one_way(tile_set_physics_layer, polygon_index);
							float one_way_collision_margin = tile_data->get_collision_polygon_one_way_margin(tile_set_physics_layer, polygon_index);
							int shapes_count = tile_data->get_collision_polygon_shapes_count(tile_set_physics_layer, polygon_index);
							for (int shape_index = 0; shape_index < shapes_count; shape_index++) {
								
								Ref<ConvexPolygonShape2D> shape = tile_data->get_collision_polygon_shape(tile_set_physics_layer, polygon_index, shape_index);
								shape = tile_map_node->get_transformed_polygon(Ref<Resource>(shape), c.alternative_tile);
								ps->body_add_shape(body, shape->get_rid());
								ps->body_set_shape_as_one_way_collision(body, body_shape_index, one_way_collision, one_way_collision_margin);
								body_shape_index++;
							}
						}