### 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_tabs->connect("tab_hovered", callable_mp(this, &EditorNode::_scene_tab_hovered));
	scene_tabs->connect("mouse_exited", callable_mp(this, &EditorNode::_scene_tab_exit));
	scene_tabs->connect("gui_input", callable_mp(this, &EditorNode::_scene_tab_input));
	scene_tabs->connect("active_tab_rearranged", callable_mp(this, &EditorNode::_reposition_active_tab));
	scene_tabs->connect("resized", callable_mp(this, &EditorNode::_update_scene_tabs));
	scene_tabs->set_h_size_flags(Control::SIZE_EXPAND_FILL);
	tabbar_container->add_child(scene_tabs);
	scene_tabs_context_menu = memnew(PopupMenu);
	tabbar_container->add_child(scene_tabs_context_menu);
	scene_tabs_context_menu->connect("id_pressed", callable_mp(this, &EditorNode::_menu_option));
	scene_tab_add = memnew(Button);
	scene_tab_add->set_flat(true);
	scene_tab_add->set_tooltip_text(TTR("Add a new scene."));
	scene_tab_add->set_icon(gui_base->get_theme_icon(SNAME("Add"), SNAME("EditorIcons")));
	scene_tab_add->add_theme_color_override("icon_normal_color", Color(0.6f, 0.6f, 0.6f, 0.8f));
	scene_tabs->add_child(scene_tab_add);
	scene_tab_add->connect("pressed", callable_mp(this, &EditorNode::_menu_option).bind(FILE_NEW_SCENE));
	scene_tab_add_ph = memnew(Control);
	scene_tab_add_ph->set_mouse_filter(Control::MOUSE_FILTER_IGNORE);
	scene_tab_add_ph->set_custom_minimum_size(scene_tab_add->get_minimum_size());
	tabbar_container->add_child(scene_tab_add_ph);
	distraction_free = memnew(Button);
	distraction_free->set_flat(true);
	ED_SHORTCUT_AND_COMMAND("editor/distraction_free_mode", TTR("Distraction Free Mode"), KeyModifierMask::CTRL | KeyModifierMask::SHIFT | Key::F11);
	ED_SHORTCUT_OVERRIDE("editor/distraction_free_mode", "macos", KeyModifierMask::META | KeyModifierMask::CTRL | Key::D);
	distraction_free->set_shortcut(ED_GET_SHORTCUT("editor/distraction_free_mode"));
	distraction_free->set_tooltip_text(TTR("Toggle distraction-free mode."));
	distraction_free->connect("pressed", callable_mp(this, &EditorNode::_toggle_distraction_free_mode));
	distraction_free->set_icon(gui_base->get_theme_icon(SNAME("DistractionFree"), SNAME("EditorIcons")));
	distraction_free->set_toggle_mode(true);