### 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)

StringName shortcut_input_group;
	StringName unhandled_input_group;
	StringName unhandled_key_input_group;
	void _update_audio_listener_2d();
	bool disable_3d = false;
	void _propagate_viewport_notification(Node *p_node, int p_what);
	void _update_global_transform();
	RID texture_rid;
	DebugDraw debug_draw = DEBUG_DRAW_DISABLED;
	int positional_shadow_atlas_size = 2048;
	bool positional_shadow_atlas_16_bits = true;
	PositionalShadowAtlasQuadrantSubdiv positional_shadow_atlas_quadrant_subdiv[4];
	MSAA msaa_2d = MSAA_DISABLED;
	MSAA msaa_3d = MSAA_DISABLED;
	ScreenSpaceAA screen_space_aa = SCREEN_SPACE_AA_DISABLED;
	bool use_taa = false;
	Scaling3DMode scaling_3d_mode = SCALING_3D_MODE_BILINEAR;
	float scaling_3d_scale = 1.0;
	float fsr_sharpness = 0.2f;
	float texture_mipmap_bias = 0.0f;
	bool use_debanding = false;
	float mesh_lod_threshold = 1.0;
	bool use_occlusion_culling = false;
	Ref<ViewportTexture> default_texture;
	HashSet<ViewportTexture *> viewport_textures;
	void _update_viewport_path();
	SDFOversize sdf_oversize = SDF_OVERSIZE_120_PERCENT;
	SDFScale sdf_scale = SDF_SCALE_50_PERCENT;
	uint32_t canvas_cull_mask = 0xffffffff; 
	enum SubWindowDrag {