### 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.
file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/new_inherited_scene", TTR("New Inherited Scene..."), KeyModifierMask::CMD_OR_CTRL + KeyModifierMask::SHIFT + Key::N), FILE_NEW_INHERITED_SCENE);
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/open_scene", TTR("Open Scene..."), KeyModifierMask::CMD_OR_CTRL + Key::O), FILE_OPEN_SCENE);
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/reopen_closed_scene", TTR("Reopen Closed Scene"), KeyModifierMask::CMD_OR_CTRL + KeyModifierMask::SHIFT + Key::T), FILE_OPEN_PREV);
	file_menu->add_submenu_item(TTR("Open Recent"), "RecentScenes", FILE_OPEN_RECENT);
	file_menu->add_separator();
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/save_scene", TTR("Save Scene"), KeyModifierMask::CMD_OR_CTRL + Key::S), FILE_SAVE_SCENE);
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/save_scene_as", TTR("Save Scene As..."), KeyModifierMask::CMD_OR_CTRL + KeyModifierMask::SHIFT + Key::S), FILE_SAVE_AS_SCENE);
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/save_all_scenes", TTR("Save All Scenes"), KeyModifierMask::CMD_OR_CTRL + KeyModifierMask::SHIFT + KeyModifierMask::ALT + Key::S), FILE_SAVE_ALL_SCENES);
	file_menu->add_separator();
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/quick_open", TTR("Quick Open..."), KeyModifierMask::SHIFT + KeyModifierMask::ALT + Key::O), FILE_QUICK_OPEN);
	ED_SHORTCUT_OVERRIDE("editor/quick_open", "macos", KeyModifierMask::META + KeyModifierMask::CTRL + Key::O);
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/quick_open_scene", TTR("Quick Open Scene..."), KeyModifierMask::CMD_OR_CTRL + KeyModifierMask::SHIFT + Key::O), FILE_QUICK_OPEN_SCENE);
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/quick_open_script", TTR("Quick Open Script..."), KeyModifierMask::CMD_OR_CTRL + KeyModifierMask::ALT + Key::O), FILE_QUICK_OPEN_SCRIPT);
	file_menu->add_separator();
	export_as_menu = memnew(PopupMenu);
	export_as_menu->set_name("Export");
	file_menu->add_child(export_as_menu);
	file_menu->add_submenu_item(TTR("Export As..."), "Export");
	export_as_menu->add_shortcut(ED_SHORTCUT("editor/export_as_mesh_library", TTR("MeshLibrary...")), FILE_EXPORT_MESH_LIBRARY);
	export_as_menu->connect("index_pressed", callable_mp(this, &EditorNode::_export_as_menu_option));
	file_menu->add_separator();
	file_menu->add_shortcut(ED_GET_SHORTCUT("ui_undo"), EDIT_UNDO, true);
	file_menu->add_shortcut(ED_GET_SHORTCUT("ui_redo"), EDIT_REDO, true);
	file_menu->add_separator();
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/reload_saved_scene", TTR("Reload Saved Scene")), EDIT_RELOAD_SAVED_SCENE);
	file_menu->add_shortcut(ED_SHORTCUT_AND_COMMAND("editor/close_scene", TTR("Close Scene"), KeyModifierMask::CMD_OR_CTRL + KeyModifierMask::SHIFT + Key::W), FILE_CLOSE);
	recent_scenes = memnew(PopupMenu);
	recent_scenes->set_name("RecentScenes");
	file_menu->add_child(recent_scenes);
	recent_scenes->connect("id_pressed", callable_mp(this, &EditorNode::_open_recent_scene));