### 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_COND(!scenes.has(p_id));
	scenes.erase(p_id);
	scenes_ids.erase(p_id);
	emit_signal(SNAME("changed"));
}
int TileSetScenesCollectionSource::get_next_scene_tile_id() const {
	return next_scene_id;
}
bool TileSetScenesCollectionSource::_set(const StringName &p_name, const Variant &p_value) {
	Vector<String> components = String(p_name).split("/", true, 2);
	if (components.size() >= 2 && components[0] == "scenes" && components[1].is_valid_int()) {
		int scene_id = components[1].to_int();
		if (components.size() >= 3 && components[2] == "scene") {
			if (has_scene_tile_id(scene_id)) {
				set_scene_tile_scene(scene_id, p_value);
			} else {
				create_scene_tile(p_value, scene_id);
			}
			return true;
		} else if (components.size() >= 3 && components[2] == "display_placeholder") {
			if (!has_scene_tile_id(scene_id)) {
				create_scene_tile(p_value, scene_id);
			}
			return true;
		}
	}
	return false;
}
bool TileSetScenesCollectionSource::_get(const StringName &p_name, Variant &r_ret) const {