### 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)
ERR_FAIL_INDEX_V(p_index, (int)patterns.size(), Ref<TileMapPattern>());
	return patterns[p_index];
}
void TileSet::remove_pattern(int p_index) {
	ERR_FAIL_INDEX(p_index, (int)patterns.size());
	patterns.remove_at(p_index);
	emit_changed();
}
int TileSet::get_patterns_count() {
	return patterns.size();
}
RBSet<TileSet::TerrainsPattern> TileSet::get_terrains_pattern_set(int p_terrain_set) {
	ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), RBSet<TileSet::TerrainsPattern>());
	_update_terrains_cache();
	RBSet<TileSet::TerrainsPattern> output;
	for (KeyValue<TileSet::TerrainsPattern, RBSet<TileMapCell>> kv : per_terrain_pattern_tiles[p_terrain_set]) {
		output.insert(kv.key);
	}
	return output;
}
RBSet<TileMapCell> TileSet::get_tiles_for_terrains_pattern(int p_terrain_set, TerrainsPattern p_terrain_tile_pattern) {