### 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)
int index = tile_data->get_collision_polygons_count(0) - 1;
								tile_data->set_collision_polygon_one_way(0, index, csd.one_way);
								tile_data->set_collision_polygon_one_way_margin(0, index, csd.one_way_margin);
								tile_data->set_collision_polygon_points(0, index, polygon);
							}
						}
					}
				}
				
				if (!compatibility_size_count.has(ctd->region.get_size())) {
					compatibility_size_count[ctd->region.get_size()] = 0;
				}
				compatibility_size_count[ctd->region.get_size()]++;
			} break;
			case COMPATIBILITY_TILE_MODE_AUTO_TILE: {
				
				WARN_PRINT_ONCE("Could not convert 3.x autotiles to 4.x. This operation cannot be done automatically, autotiles must be re-created using the terrain system.");
			} break;
			case COMPATIBILITY_TILE_MODE_ATLAS_TILE: {
				atlas_source->set_margins(ctd->region.get_position());
				atlas_source->set_separation(Vector2i(ctd->autotile_spacing, ctd->autotile_spacing));
				atlas_source->set_texture_region_size(ctd->autotile_tile_size);
				Size2i atlas_size = ctd->region.get_size() / (ctd->autotile_tile_size + atlas_source->get_separation());
				for (int i = 0; i < atlas_size.x; i++) {
					for (int j = 0; j < atlas_size.y; j++) {
						Vector2i coords = Vector2i(i, j);
						for (int flags = 0; flags < 8; flags++) {
							bool flip_h = flags & 1;
							bool flip_v = flags & 2;
							bool transpose = flags & 4;