### 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.
main_menu->set_prefer_global_menu(global_menu);
	main_menu->set_switch_on_hover(true);
	file_menu = memnew(PopupMenu);
	file_menu->set_name(TTR("Scene"));
	main_menu->add_child(file_menu);
	main_menu->set_menu_tooltip(0, TTR("Operations with scene files."));
	prev_scene = memnew(Button);
	prev_scene->set_flat(true);
	prev_scene->set_icon(gui_base->get_theme_icon(SNAME("PrevScene"), SNAME("EditorIcons")));
	prev_scene->set_tooltip_text(TTR("Go to previously opened scene."));
	prev_scene->set_disabled(true);
	prev_scene->connect("pressed", callable_mp(this, &EditorNode::_menu_option).bind(FILE_OPEN_PREV));
	gui_base->add_child(prev_scene);
	prev_scene->set_position(Point2(3, 24));
	prev_scene->hide();
	accept = memnew(AcceptDialog);
	accept->set_unparent_when_invisible(true);
	save_accept = memnew(AcceptDialog);
	save_accept->set_unparent_when_invisible(true);
	save_accept->connect("confirmed", callable_mp(this, &EditorNode::_menu_option).bind((int)MenuOptions::FILE_SAVE_AS_SCENE));
	project_export = memnew(ProjectExportDialog);
	gui_base->add_child(project_export);
	dependency_error = memnew(DependencyErrorDialog);
	gui_base->add_child(dependency_error);
	dependency_fixer = memnew(DependencyEditor);
	gui_base->add_child(dependency_fixer);
	editor_settings_dialog = memnew(EditorSettingsDialog);
	gui_base->add_child(editor_settings_dialog);
	project_settings_editor = memnew(ProjectSettingsEditor(&editor_data));
	gui_base->add_child(project_settings_editor);