### 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.
project_menu->add_child(vcs_actions_menu);
	project_menu->set_item_submenu(project_menu->get_item_index(VCS_MENU), "Version Control");
	add_editor_plugin(memnew(AudioBusesEditorPlugin(audio_bus_editor)));
	for (int i = 0; i < EditorPlugins::get_plugin_count(); i++) {
		add_editor_plugin(EditorPlugins::create(i));
	}
	for (const StringName &extension_class_name : GDExtensionEditorPlugins::get_extension_classes()) {
		add_extension_editor_plugin(extension_class_name);
	}
	GDExtensionEditorPlugins::editor_node_add_plugin = &EditorNode::add_extension_editor_plugin;
	GDExtensionEditorPlugins::editor_node_remove_plugin = &EditorNode::remove_extension_editor_plugin;
	for (int i = 0; i < plugin_init_callback_count; i++) {
		plugin_init_callbacks[i]();
	}
	resource_preview->add_preview_generator(Ref<EditorTexturePreviewPlugin>(memnew(EditorTexturePreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorImagePreviewPlugin>(memnew(EditorImagePreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorPackedScenePreviewPlugin>(memnew(EditorPackedScenePreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorMaterialPreviewPlugin>(memnew(EditorMaterialPreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorScriptPreviewPlugin>(memnew(EditorScriptPreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorAudioStreamPreviewPlugin>(memnew(EditorAudioStreamPreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorMeshPreviewPlugin>(memnew(EditorMeshPreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorBitmapPreviewPlugin>(memnew(EditorBitmapPreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorFontPreviewPlugin>(memnew(EditorFontPreviewPlugin)));
	resource_preview->add_preview_generator(Ref<EditorGradientPreviewPlugin>(memnew(EditorGradientPreviewPlugin)));
	{
		Ref<StandardMaterial3DConversionPlugin> spatial_mat_convert;
		spatial_mat_convert.instantiate();
		resource_conversion_plugins.push_back(spatial_mat_convert);
		Ref<ORMMaterial3DConversionPlugin> orm_mat_convert;
		orm_mat_convert.instantiate();