### 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.
_screenshot();
}
void EditorNode::_screenshot(bool p_use_utc) {
	String name = "editor_screenshot_" + Time::get_singleton()->get_datetime_string_from_system(p_use_utc).replace(":", "") + ".png";
	NodePath path = String("user:") + name;
	_save_screenshot(path);
	if (EDITOR_GET("interface/editor/automatically_open_screenshots")) {
		OS::get_singleton()->shell_show_in_file_manager(ProjectSettings::get_singleton()->globalize_path(path), true);
	}
}
void EditorNode::_save_screenshot(NodePath p_path) {
	Control *editor_main_screen = EditorInterface::get_singleton()->get_editor_main_screen();
	ERR_FAIL_COND_MSG(!editor_main_screen, "Cannot get the editor main screen control.");
	Viewport *viewport = editor_main_screen->get_viewport();
	ERR_FAIL_COND_MSG(!viewport, "Cannot get a viewport from the editor main screen.");
	Ref<ViewportTexture> texture = viewport->get_texture();
	ERR_FAIL_COND_MSG(texture.is_null(), "Cannot get a viewport texture from the editor main screen.");
	Ref<Image> img = texture->get_image();
	ERR_FAIL_COND_MSG(img.is_null(), "Cannot get an image from a viewport texture of the editor main screen.");
	Error error = img->save_png(p_path);
	ERR_FAIL_COND_MSG(error != OK, "Cannot save screenshot to file '" + p_path + "'.");
}
void EditorNode::_tool_menu_option(int p_idx) {