### 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.
tab_preview_panel->hide();
}
void EditorNode::_scene_tab_input(const Ref<InputEvent> &p_input) {
	Ref<InputEventMouseButton> mb = p_input;
	if (mb.is_valid()) {
		if (scene_tabs->get_hovered_tab() >= 0) {
			if (mb->get_button_index() == MouseButton::MIDDLE && mb->is_pressed()) {
				_scene_tab_closed(scene_tabs->get_hovered_tab());
			}
		} else if (mb->get_button_index() == MouseButton::LEFT && mb->is_double_click()) {
			int tab_buttons = 0;
			if (scene_tabs->get_offset_buttons_visible()) {
				tab_buttons = theme->get_icon(SNAME("increment"), SNAME("TabBar"))->get_width() + theme->get_icon(SNAME("decrement"), SNAME("TabBar"))->get_width();
			}
			if ((gui_base->is_layout_rtl() && mb->get_position().x > tab_buttons) || (!gui_base->is_layout_rtl() && mb->get_position().x < scene_tabs->get_size().width - tab_buttons)) {
				_menu_option_confirm(FILE_NEW_SCENE, true);
			}
		}
		if (mb->get_button_index() == MouseButton::RIGHT && mb->is_pressed()) {
			
			scene_tabs_context_menu->clear();