### 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)
}
				return false;
			} else if (components[1].is_valid_int()) {
				int alternative_id = components[1].to_int();
				if (alternative_id != TileSetSource::INVALID_TILE_ALTERNATIVE) {
					
					if (!has_alternative_tile(coords, alternative_id)) {
						create_alternative_tile(coords, alternative_id);
					}
					if (!tiles[coords].alternatives.has(alternative_id)) {
						tiles[coords].alternatives[alternative_id] = memnew(TileData);
						tiles[coords].alternatives[alternative_id]->set_tile_set(tile_set);
						tiles[coords].alternatives[alternative_id]->set_allow_transform(alternative_id > 0);
						tiles[coords].alternatives_ids.push_back(alternative_id);
					}
					if (components.size() >= 3) {
						bool valid;
						tiles[coords].alternatives[alternative_id]->set(components[2], p_value, &valid);
						return valid;
					} else {
						
						return true;
					}
				}
			}
		}
	}
	return false;
}
bool TileSetAtlasSource::_get(const StringName &p_name, Variant &r_ret) const {