### 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.
case FILE_EXPORT_PROJECT: {
			project_export->popup_export();
		} break;
		case FILE_EXTERNAL_OPEN_SCENE: {
			if (unsaved_cache && !p_confirmed) {
				confirmation->set_ok_button_text(TTR("Open"));
				confirmation->set_text(TTR("Current scene not saved. Open anyway?"));
				confirmation->popup_centered();
				break;
			}
			bool oprev = opening_prev;
			Error err = load_scene(external_file);
			if (err == OK && oprev) {
				previous_scenes.pop_back();
				opening_prev = false;
			}
		} break;
		case EDIT_UNDO: {
			if ((int)Input::get_singleton()->get_mouse_button_mask() & 0x7) {
				log->add_message(TTR("Can't undo while mouse buttons are pressed."), EditorLog::MSG_TYPE_EDITOR);
			} else {
				EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
				String action = undo_redo->get_current_action_name();
				int id = undo_redo->get_current_action_history_id();
				if (!undo_redo->undo()) {
					log->add_message(TTR("Nothing to undo."), EditorLog::MSG_TYPE_EDITOR);
				} else if (!action.is_empty()) {
					switch (id) {
						case EditorUndoRedoManager::GLOBAL_HISTORY:
							log->add_message(vformat(TTR("Global Undo: %s"), action), EditorLog::MSG_TYPE_EDITOR);