### 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.
center_split->connect("resized", callable_mp(this, &EditorNode::_vp_resized));
	native_shader_source_visualizer = memnew(EditorNativeShaderSourceVisualizer);
	gui_base->add_child(native_shader_source_visualizer);
	orphan_resources = memnew(OrphanResourcesDialog);
	gui_base->add_child(orphan_resources);
	confirmation = memnew(ConfirmationDialog);
	gui_base->add_child(confirmation);
	confirmation->connect("confirmed", callable_mp(this, &EditorNode::_menu_confirm_current));
	save_confirmation = memnew(ConfirmationDialog);
	save_confirmation->add_button(TTR("Don't Save"), DisplayServer::get_singleton()->get_swap_cancel_ok(), "discard");
	gui_base->add_child(save_confirmation);
	save_confirmation->set_min_size(Vector2(450.0 * EDSCALE, 0));
	save_confirmation->connect("confirmed", callable_mp(this, &EditorNode::_menu_confirm_current));
	save_confirmation->connect("custom_action", callable_mp(this, &EditorNode::_discard_changes));
	gradle_build_manage_templates = memnew(ConfirmationDialog);
	gradle_build_manage_templates->set_text(TTR("Android build template is missing, please install relevant templates."));
	gradle_build_manage_templates->set_ok_button_text(TTR("Manage Templates"));
	gradle_build_manage_templates->add_button(TTR("Install from file"))->connect("pressed", callable_mp(this, &EditorNode::_menu_option).bind(SETTINGS_INSTALL_ANDROID_BUILD_TEMPLATE));
	gradle_build_manage_templates->connect("confirmed", callable_mp(this, &EditorNode::_menu_option).bind(SETTINGS_MANAGE_EXPORT_TEMPLATES));
	gui_base->add_child(gradle_build_manage_templates);
	file_android_build_source = memnew(EditorFileDialog);
	file_android_build_source->set_title(TTR("Select Android sources file"));
	file_android_build_source->set_access(EditorFileDialog::ACCESS_FILESYSTEM);
	file_android_build_source->set_file_mode(EditorFileDialog::FILE_MODE_OPEN_FILE);
	file_android_build_source->add_filter("*.zip");
	file_android_build_source->connect("file_selected", callable_mp(this, &EditorNode::_android_build_source_selected));
	gui_base->add_child(file_android_build_source);
	install_android_build_template = memnew(ConfirmationDialog);
	install_android_build_template->set_text(TTR("This will set up your project for gradle Android builds by installing the source template to \"res:android/build\".\nYou can then apply modifications and build your own custom APK on export (adding modules, changing the AndroidManifest.xml, etc.).\nNote that in order to make gradle builds instead of using pre-built APKs, the \"Use Gradle Build\" option should be enabled in the Android export preset."));
	install_android_build_template->set_ok_button_text(TTR("Install"));