### 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)
}
					}
				}
				
				if (!compatibility_size_count.has(ctd->region.get_size())) {
					compatibility_size_count[ctd->autotile_tile_size] = 0;
				}
				compatibility_size_count[ctd->autotile_tile_size] += atlas_size.x * atlas_size.y;
			} break;
		}
		
		for (int k = 0; k < ctd->shapes.size(); k++) {
			Ref<ConvexPolygonShape2D> convex = ctd->shapes[k].shape;
			if (convex.is_valid()) {
				Vector<Vector2> points = convex->get_points();
				for (int i_point = 0; i_point < points.size(); i_point++) {
					points.write[i_point] = points[i_point] - get_tile_size() / 2;
				}
				convex->set_points(points);
			}
		}
	}
	
	Vector2i max_size = get_tile_size();
	int max_count = 0;
	for (KeyValue<Vector2i, int> kv : compatibility_size_count) {
		if (kv.value > max_count) {