### 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.
execute_outputs->set_context_menu_enabled(true);
	execute_output_dialog = memnew(AcceptDialog);
	execute_output_dialog->set_unparent_when_invisible(true);
	execute_output_dialog->add_child(execute_outputs);
	execute_output_dialog->set_title("");
	EditorFileSystem::get_singleton()->connect("sources_changed", callable_mp(this, &EditorNode::_sources_changed));
	EditorFileSystem::get_singleton()->connect("filesystem_changed", callable_mp(this, &EditorNode::_fs_changed));
	EditorFileSystem::get_singleton()->connect("resources_reimported", callable_mp(this, &EditorNode::_resources_reimported));
	EditorFileSystem::get_singleton()->connect("resources_reload", callable_mp(this, &EditorNode::_resources_changed));
	_build_icon_type_cache();
	pick_main_scene = memnew(ConfirmationDialog);
	gui_base->add_child(pick_main_scene);
	pick_main_scene->set_ok_button_text(TTR("Select"));
	pick_main_scene->connect("confirmed", callable_mp(this, &EditorNode::_menu_option).bind(SETTINGS_PICK_MAIN_SCENE));
	select_current_scene_button = pick_main_scene->add_button(TTR("Select Current"), true, "select_current");
	pick_main_scene->connect("custom_action", callable_mp(this, &EditorNode::_pick_main_scene_custom_action));
	for (int i = 0; i < _init_callbacks.size(); i++) {
		_init_callbacks[i]();
	}
	editor_data.add_edited_scene(-1);
	editor_data.set_edited_scene(0);
	_update_scene_tabs();
	ImportDock::get_singleton()->initialize_import_options();
	FileAccess::set_file_close_fail_notify_callback(_file_access_close_error_notify);
	print_handler.printfunc = _print_handler;
	print_handler.userdata = this;
	add_print_handler(&print_handler);
	ResourceSaver::set_save_callback(_resource_saved);
	ResourceLoader::set_load_callback(_resource_loaded);