### 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(!scenes.has(p_id), Ref<PackedScene>());
	return scenes[p_id].scene;
}
void TileSetScenesCollectionSource::set_scene_tile_display_placeholder(int p_id, bool p_display_placeholder) {
	ERR_FAIL_COND(!scenes.has(p_id));
	scenes[p_id].display_placeholder = p_display_placeholder;
	emit_signal(SNAME("changed"));
}
bool TileSetScenesCollectionSource::get_scene_tile_display_placeholder(int p_id) const {
	ERR_FAIL_COND_V(!scenes.has(p_id), false);
	return scenes[p_id].display_placeholder;
}
void TileSetScenesCollectionSource::remove_scene_tile(int p_id) {