### Godot version

v4.1.1.stable.mono.official [bd6af8e0e]

### System information

Godot v4.1.1.stable.mono - macOS 13.4.1 - Vulkan (Forward+) - integrated Apple M1 - Apple M1 (8 Threads)

### Issue description

After creating a `@tool` script that is autoloaded and uses Semaphores and a Thread, when exiting the editor it freezes and stops responding on MacOS.

Editor not responding after closing the editor:
![image](https://github.com/godotengine/godot/assets/29845000/1a08e748-5ca9-4ed1-9bf0-a1399aab7629)
![image](https://github.com/godotengine/godot/assets/29845000/fa60171c-3123-4e85-b3ca-ab806d4f7bde)

The editor must then be force quit and produces the following error information:
https://gist.github.com/Trikzon/dc3e1ed7a258fa9cc2c363b18b43c353

A full minimal reproducible product is provided, but the important snippets are:
```
@tool
extends Node

var mutex: Mutex
var semaphore: Semaphore
var thread: Thread
var exit_thread := false


func _ready():
    mutex = Mutex.new()
    semaphore = Semaphore.new()
    exit_thread = false
    
    thread = Thread.new()
    thread.start(_thread_function)

func _thread_function():
    while true:
        semaphore.wait()
        
        mutex.lock()
        var should_exit = exit_thread
        mutex.unlock()
        
        if should_exit:
            break
        
       # Actual thread work goes here

func _exit_tree():
    mutex.lock()
    exit_thread = true
    mutex.unlock()
    
    semaphore.post()
    
    thread.wait_to_finish()
```

At first I thought that `_exit_tree()` was not being called when the editor closed, but I found that it is because placing a `ResourceSaver.save()` in `_exit_tree()` creates a file when the editor closes.

### Steps to reproduce

Create a `@tool` script using Semaphores and a Thread and set it as an autoloading script in-editor.

The [Using Multiple Threads#Semaphores](https://docs.godotengine.org/en/stable/tutorials/performance/using_multiple_threads.html#semaphores) guide can be used as a base.

### Minimal reproduction project

[Thread Tools Test.zip](https://github.com/godotengine/godot/files/12237193/Thread.Tools.Test.zip)

Note: I use a mono build of Godot, but this does not contain any C#.

Contains an autoloaded tool script that is a slightly modified version of the [Using Multiple Threads#Semaphores](https://docs.godotengine.org/en/stable/tutorials/performance/using_multiple_threads.html#semaphores) guide.

Also contains a test scene with a tool script where changing a number in-editor will post the semaphore to see that the thread is running correctly in the background.
scene_root->set_snap_2d_transforms_to_pixel(snap_2d_transforms);
	bool snap_2d_vertices = GLOBAL_GET("rendering/2d/snap/snap_2d_vertices_to_pixel");
	scene_root->set_snap_2d_vertices_to_pixel(snap_2d_vertices);
	Viewport::SDFOversize sdf_oversize = Viewport::SDFOversize(int(GLOBAL_GET("rendering/2d/sdf/oversize")));
	scene_root->set_sdf_oversize(sdf_oversize);
	Viewport::SDFScale sdf_scale = Viewport::SDFScale(int(GLOBAL_GET("rendering/2d/sdf/scale")));
	scene_root->set_sdf_scale(sdf_scale);
	Viewport::MSAA msaa = Viewport::MSAA(int(GLOBAL_GET("rendering/anti_aliasing/quality/msaa_2d")));
	scene_root->set_msaa_2d(msaa);
	float mesh_lod_threshold = GLOBAL_GET("rendering/mesh_lod/lod_change/threshold_pixels");
	scene_root->set_mesh_lod_threshold(mesh_lod_threshold);
	RS::get_singleton()->decals_set_filter(RS::DecalFilter(int(GLOBAL_GET("rendering/textures/decals/filter"))));
	RS::get_singleton()->light_projectors_set_filter(RS::LightProjectorFilter(int(GLOBAL_GET("rendering/textures/light_projectors/filter"))));
	SceneTree *tree = get_tree();
	tree->set_debug_collisions_color(GLOBAL_GET("debug/shapes/collision/shape_color"));
	tree->set_debug_collision_contact_color(GLOBAL_GET("debug/shapes/collision/contact_color"));
#ifdef DEBUG_ENABLED
	NavigationServer3D::get_singleton()->set_debug_navigation_edge_connection_color(GLOBAL_GET("debug/shapes/navigation/edge_connection_color"));
	NavigationServer3D::get_singleton()->set_debug_navigation_geometry_edge_color(GLOBAL_GET("debug/shapes/navigation/geometry_edge_color"));
	NavigationServer3D::get_singleton()->set_debug_navigation_geometry_face_color(GLOBAL_GET("debug/shapes/navigation/geometry_face_color"));
	NavigationServer3D::get_singleton()->set_debug_navigation_geometry_edge_disabled_color(GLOBAL_GET("debug/shapes/navigation/geometry_edge_disabled_color"));
	NavigationServer3D::get_singleton()->set_debug_navigation_geometry_face_disabled_color(GLOBAL_GET("debug/shapes/navigation/geometry_face_disabled_color"));
	NavigationServer3D::get_singleton()->set_debug_navigation_enable_edge_connections(GLOBAL_GET("debug/shapes/navigation/enable_edge_connections"));
	NavigationServer3D::get_singleton()->set_debug_navigation_enable_edge_connections_xray(GLOBAL_GET("debug/shapes/navigation/enable_edge_connections_xray"));
	NavigationServer3D::get_singleton()->set_debug_navigation_enable_edge_lines(GLOBAL_GET("debug/shapes/navigation/enable_edge_lines"));
	NavigationServer3D::get_singleton()->set_debug_navigation_enable_edge_lines_xray(GLOBAL_GET("debug/shapes/navigation/enable_edge_lines_xray"));
	NavigationServer3D::get_singleton()->set_debug_navigation_enable_geometry_face_random_color(GLOBAL_GET("debug/shapes/navigation/enable_geometry_face_random_color"));
#endif 
}
void EditorNode::_select_default_main_screen_plugin() {