### 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.
progress_hb = memnew(BackgroundProgress);
	layout_dialog = memnew(EditorLayoutsDialog);
	gui_base->add_child(layout_dialog);
	layout_dialog->set_hide_on_ok(false);
	layout_dialog->set_size(Size2(225, 270) * EDSCALE);
	layout_dialog->connect("name_confirmed", callable_mp(this, &EditorNode::_dialog_action));
	update_spinner = memnew(MenuButton);
	right_menu_hb->add_child(update_spinner);
	update_spinner->set_icon(gui_base->get_theme_icon(SNAME("Progress1"), SNAME("EditorIcons")));
	update_spinner->get_popup()->connect("id_pressed", callable_mp(this, &EditorNode::_menu_option));
	PopupMenu *p = update_spinner->get_popup();
	p->add_radio_check_item(TTR("Update Continuously"), SETTINGS_UPDATE_CONTINUOUSLY);
	p->add_radio_check_item(TTR("Update When Changed"), SETTINGS_UPDATE_WHEN_CHANGED);
	p->add_separator();
	p->add_item(TTR("Hide Update Spinner"), SETTINGS_UPDATE_SPINNER_HIDE);
	_update_update_spinner();
	
	memnew(SceneTreeDock(scene_root, editor_selection, editor_data));
	memnew(InspectorDock(editor_data));
	memnew(ImportDock);
	memnew(NodeDock);
	FileSystemDock *filesystem_dock = memnew(FileSystemDock);
	filesystem_dock->connect("inherit", callable_mp(this, &EditorNode::_inherit_request));
	filesystem_dock->connect("instantiate", callable_mp(this, &EditorNode::_instantiate_request));
	filesystem_dock->connect("display_mode_changed", callable_mp(this, &EditorNode::_save_editor_layout));
	get_project_settings()->connect_filesystem_dock_signals(filesystem_dock);
	history_dock = memnew(HistoryDock);
	
	dock_slot[DOCK_SLOT_LEFT_UR]->add_child(SceneTreeDock::get_singleton());
	dock_slot[DOCK_SLOT_LEFT_UR]->set_tab_title(dock_slot[DOCK_SLOT_LEFT_UR]->get_tab_idx_from_control(SceneTreeDock::get_singleton()), TTR("Scene"));