### 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.
disambiguated_scene_names.append(editor_data.get_scene_title(i));
		full_path_names.append(editor_data.get_scene_path(i));
	}
	disambiguate_filenames(full_path_names, disambiguated_scene_names);
	
	scene_tabs->disconnect("tab_changed", callable_mp(this, &EditorNode::_scene_tab_changed));
	scene_tabs->clear_tabs();
	Ref<Texture2D> script_icon = gui_base->get_theme_icon(SNAME("Script"), SNAME("EditorIcons"));
	for (int i = 0; i < editor_data.get_edited_scene_count(); i++) {
		Node *type_node = editor_data.get_edited_scene_root(i);
		Ref<Texture2D> icon;
		if (type_node) {
			icon = EditorNode::get_singleton()->get_object_icon(type_node, "Node");
		}
		bool unsaved = EditorUndoRedoManager::get_singleton()->is_history_unsaved(editor_data.get_scene_history_id(i));
		scene_tabs->add_tab(disambiguated_scene_names[i] + (unsaved ? "(*)" : ""), icon);
		if (DisplayServer::get_singleton()->has_feature(DisplayServer::FEATURE_GLOBAL_MENU)) {
			DisplayServer::get_singleton()->global_menu_add_item("_dock", editor_data.get_scene_title(i) + (unsaved ? "(*)" : ""), callable_mp(this, &EditorNode::_global_menu_scene), Callable(), i);
		}
		if (show_rb && editor_data.get_scene_root_script(i).is_valid()) {
			scene_tabs->set_tab_button_icon(i, script_icon);
		}
	}
	if (DisplayServer::get_singleton()->has_feature(DisplayServer::FEATURE_GLOBAL_MENU)) {
		DisplayServer::get_singleton()->global_menu_add_separator("_dock");
		DisplayServer::get_singleton()->global_menu_add_item("_dock", TTR("New Window"), callable_mp(this, &EditorNode::_global_menu_new_window));
	}
	if (scene_tabs->get_tab_count() > 0) {
		scene_tabs->set_current_tab(editor_data.get_edited_scene());
	}