### 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_V(p_atlas_coords != Vector2i(), false);
	return scenes.has(p_alternative_tile);
}
int TileSetScenesCollectionSource::create_scene_tile(Ref<PackedScene> p_packed_scene, int p_id_override) {
	ERR_FAIL_COND_V_MSG(p_id_override >= 0 && scenes.has(p_id_override), INVALID_TILE_ALTERNATIVE, vformat("Cannot create scene tile. Another scene tile exists with id %d.", p_id_override));
	int new_scene_id = p_id_override >= 0 ? p_id_override : next_scene_id;
	scenes[new_scene_id] = SceneData();
	scenes_ids.push_back(new_scene_id);
	scenes_ids.sort();
	set_scene_tile_scene(new_scene_id, p_packed_scene);
	_compute_next_alternative_id();
	emit_signal(SNAME("changed"));
	return new_scene_id;
}
void TileSetScenesCollectionSource::set_scene_tile_id(int p_id, int p_new_id) {
	ERR_FAIL_COND(p_new_id < 0);
	ERR_FAIL_COND(!has_scene_tile_id(p_id));
	ERR_FAIL_COND(has_scene_tile_id(p_new_id));
	scenes[p_new_id] = SceneData();
	scenes[p_new_id] = scenes[p_id];
	scenes_ids.push_back(p_new_id);
	scenes_ids.sort();
	_compute_next_alternative_id();
	scenes.erase(p_id);
	scenes_ids.erase(p_id);
	emit_signal(SNAME("changed"));
}
void TileSetScenesCollectionSource::set_scene_tile_scene(int p_id, Ref<PackedScene> p_packed_scene) {