### 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.
ED_SHORTCUT_AND_COMMAND("editor/editor_2d", TTR("Open 2D Editor"), KeyModifierMask::CTRL | Key::F1);
	ED_SHORTCUT_AND_COMMAND("editor/editor_3d", TTR("Open 3D Editor"), KeyModifierMask::CTRL | Key::F2);
	ED_SHORTCUT_AND_COMMAND("editor/editor_script", TTR("Open Script Editor"), KeyModifierMask::CTRL | Key::F3);
	ED_SHORTCUT_AND_COMMAND("editor/editor_assetlib", TTR("Open Asset Library"), KeyModifierMask::CTRL | Key::F4);
	ED_SHORTCUT_OVERRIDE("editor/editor_2d", "macos", KeyModifierMask::META | KeyModifierMask::CTRL | Key::KEY_1);
	ED_SHORTCUT_OVERRIDE("editor/editor_3d", "macos", KeyModifierMask::META | KeyModifierMask::CTRL | Key::KEY_2);
	ED_SHORTCUT_OVERRIDE("editor/editor_script", "macos", KeyModifierMask::META | KeyModifierMask::CTRL | Key::KEY_3);
	ED_SHORTCUT_OVERRIDE("editor/editor_assetlib", "macos", KeyModifierMask::META | KeyModifierMask::CTRL | Key::KEY_4);
	ED_SHORTCUT_AND_COMMAND("editor/editor_next", TTR("Open the next Editor"));
	ED_SHORTCUT_AND_COMMAND("editor/editor_prev", TTR("Open the previous Editor"));
	screenshot_timer = memnew(Timer);
	screenshot_timer->set_one_shot(true);
	screenshot_timer->set_wait_time(settings_menu->get_submenu_popup_delay() + 0.1f);
	screenshot_timer->connect("timeout", callable_mp(this, &EditorNode::_request_screenshot));
	add_child(screenshot_timer);
	screenshot_timer->set_owner(get_owner());
	
	int max_w = MAX(project_run_bar->get_minimum_size().x + right_menu_hb->get_minimum_size().x, main_menu->get_minimum_size().x);
	left_spacer->set_custom_minimum_size(Size2(MAX(0, max_w - main_menu->get_minimum_size().x), 0));
	right_spacer->set_custom_minimum_size(Size2(MAX(0, max_w - project_run_bar->get_minimum_size().x - right_menu_hb->get_minimum_size().x), 0));
	
	if (can_expand) {
		DisplayServer::get_singleton()->window_set_flag(DisplayServer::WINDOW_FLAG_EXTEND_TO_TITLE, true, DisplayServer::MAIN_WINDOW_ID);
		title_bar->set_can_move_window(true);
	}
	String exec = OS::get_singleton()->get_executable_path();
	
	EditorSettings::get_singleton()->set_project_metadata("editor_metadata", "executable_path", exec);
}
EditorNode::~EditorNode() {