### Godot version

4.0.stable

### System information

Windows 10

### Issue description

In my project, we are rendering a GUI to a QuadMesh as an in-game interactive display. We push mouse click events when the player clicks the display. This worked fine during 4.0 beta, but after moving to the stable release the buttons on TreeItems stopped working. I put together a MRP and went back through the versions and it seems the issue started in RC1.

### Steps to reproduce

When running the MRP, it has a standard GUI on the left hand side of the screen and a QuadMesh rendered GUI on the right hand side. If you click the + button on an item, it will add another item to the list. On the QuadMesh you will see that you can highlight and collapse items in the list, but the + button does not function. If you run the MRP on 4.0.beta17 everything will function as expected.

### Minimal reproduction project

[TreeUI_through_SubViewport.zip](https://github.com/godotengine/godot/files/10959159/TreeUI_through_SubViewport.zip)

AudioListener2D *get_audio_listener_2d() const;
	Camera2D *get_camera_2d() const;
	void set_as_audio_listener_2d(bool p_enable);
	bool is_audio_listener_2d() const;
	void update_canvas_items();
	Rect2 get_visible_rect() const;
	RID get_viewport_rid() const;
	void set_world_2d(const Ref<World2D> &p_world_2d);
	Ref<World2D> get_world_2d() const;
	Ref<World2D> find_world_2d() const;
	void enable_canvas_transform_override(bool p_enable);
	bool is_canvas_transform_override_enbled() const;
	void set_canvas_transform_override(const Transform2D &p_transform);
	Transform2D get_canvas_transform_override() const;
	void set_canvas_transform(const Transform2D &p_transform);
	Transform2D get_canvas_transform() const;
	void set_global_canvas_transform(const Transform2D &p_transform);
	Transform2D get_global_canvas_transform() const;
	virtual Transform2D get_final_transform() const;
	void assign_next_enabled_camera_2d(const StringName &p_camera_group);
	void gui_set_root_order_dirty();
	void set_transparent_background(bool p_enable);
	bool has_transparent_background() const;
	Ref<ViewportTexture> get_texture() const;