### 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.
version_info_vbc->add_child(v_spacer);
	version_btn = memnew(LinkButton);
	version_btn->set_text(VERSION_FULL_CONFIG);
	String hash = String(VERSION_HASH);
	if (hash.length() != 0) {
		hash = " " + vformat("[%s]", hash.left(9));
	}
	
	version_btn->set_meta(META_TEXT_TO_COPY, "v" VERSION_FULL_BUILD + hash);
	
	version_btn->set_self_modulate(Color(1, 1, 1, 0.65));
	version_btn->set_underline_mode(LinkButton::UNDERLINE_MODE_ON_HOVER);
	version_btn->set_tooltip_text(TTR("Click to copy."));
	version_btn->connect("pressed", callable_mp(this, &EditorNode::_version_button_pressed));
	version_info_vbc->add_child(version_btn);
	
	Control *h_spacer = memnew(Control);
	bottom_panel_hb->add_child(h_spacer);
	bottom_panel_raise = memnew(Button);
	bottom_panel_raise->set_flat(true);
	bottom_panel_raise->set_icon(gui_base->get_theme_icon(SNAME("ExpandBottomDock"), SNAME("EditorIcons")));
	bottom_panel_raise->set_shortcut(ED_SHORTCUT_AND_COMMAND("editor/bottom_panel_expand", TTR("Expand Bottom Panel"), KeyModifierMask::SHIFT | Key::F12));
	bottom_panel_hb->add_child(bottom_panel_raise);
	bottom_panel_raise->hide();
	bottom_panel_raise->set_toggle_mode(true);
	bottom_panel_raise->connect("toggled", callable_mp(this, &EditorNode::_bottom_panel_raise_toggled));
	log = memnew(EditorLog);
	Button *output_button = add_bottom_panel_item(TTR("Output"), log);
	output_button->set_theme_type_variation("BottomPanelButton");
	log->set_tool_button(output_button);