### 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)
#ifndef DISABLE_DEPRECATED
	for (const KeyValue<int, CompatibilityTileData *> &E : compatibility_data) {
		memdelete(E.value);
	}
#endif 
	while (!source_ids.is_empty()) {
		remove_source(source_ids[0]);
	}
}
void TileSetSource::set_tile_set(const TileSet *p_tile_set) {
	tile_set = p_tile_set;
}
TileSet *TileSetSource::get_tile_set() const {
	return (TileSet *)tile_set;
}
void TileSetSource::reset_state() {
	tile_set = nullptr;
};
void TileSetSource::_bind_methods() {
	
	ClassDB::bind_method(D_METHOD("get_tiles_count"), &TileSetSource::get_tiles_count);
	ClassDB::bind_method(D_METHOD("get_tile_id", "index"), &TileSetSource::get_tile_id);
	ClassDB::bind_method(D_METHOD("has_tile", "atlas_coords"), &TileSetSource::has_tile);
	
	ClassDB::bind_method(D_METHOD("get_alternative_tiles_count", "atlas_coords"), &TileSetSource::get_alternative_tiles_count);
	ClassDB::bind_method(D_METHOD("get_alternative_tile_id", "atlas_coords", "index"), &TileSetSource::get_alternative_tile_id);
	ClassDB::bind_method(D_METHOD("has_alternative_tile", "atlas_coords", "alternative_tile"), &TileSetSource::has_alternative_tile);
}
void TileSetAtlasSource::set_tile_set(const TileSet *p_tile_set) {