### 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(p_from_index, physics_layers.size());
	ERR_FAIL_INDEX(p_to_pos, physics_layers.size() + 1);
	physics_layers.insert(p_to_pos, physics_layers[p_from_index]);
	physics_layers.remove_at(p_to_pos < p_from_index ? p_from_index + 1 : p_from_index);
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->move_physics_layer(p_from_index, p_to_pos);
	}
	notify_property_list_changed();
	emit_changed();
}
void TileSet::remove_physics_layer(int p_index) {
	ERR_FAIL_INDEX(p_index, physics_layers.size());
	physics_layers.remove_at(p_index);
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->remove_physics_layer(p_index);
	}
	notify_property_list_changed();
	emit_changed();
}
void TileSet::set_physics_layer_collision_layer(int p_layer_index, uint32_t p_layer) {