### 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_index, navigation_layers.size());
	navigation_layers.remove_at(p_index);
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->remove_navigation_layer(p_index);
	}
	notify_property_list_changed();
	emit_changed();
}
void TileSet::set_navigation_layer_layers(int p_layer_index, uint32_t p_layers) {
	ERR_FAIL_INDEX(p_layer_index, navigation_layers.size());
	navigation_layers.write[p_layer_index].layers = p_layers;
	emit_changed();
}
uint32_t TileSet::get_navigation_layer_layers(int p_layer_index) const {
	ERR_FAIL_INDEX_V(p_layer_index, navigation_layers.size(), 0);
	return navigation_layers[p_layer_index].layers;
}
void TileSet::set_navigation_layer_layer_value(int p_layer_index, int p_layer_number, bool p_value) {
	ERR_FAIL_COND_MSG(p_layer_number < 1, "Navigation layer number must be between 1 and 32 inclusive.");
	ERR_FAIL_COND_MSG(p_layer_number > 32, "Navigation layer number must be between 1 and 32 inclusive.");
	uint32_t _navigation_layers = get_navigation_layer_layers(p_layer_index);
	if (p_value) {
		_navigation_layers |= 1 << (p_layer_number - 1);
	} else {
		_navigation_layers &= ~(1 << (p_layer_number - 1));
	}
	set_navigation_layer_layers(p_layer_index, _navigation_layers);
}
bool TileSet::get_navigation_layer_layer_value(int p_layer_index, int p_layer_number) const {