### 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.
install_android_build_template->connect("confirmed", callable_mp(this, &EditorNode::_menu_confirm_current));
	gui_base->add_child(install_android_build_template);
	remove_android_build_template = memnew(ConfirmationDialog);
	remove_android_build_template->set_text(TTR("The Android build template is already installed in this project and it won't be overwritten.\nRemove the \"res:android/build\" directory manually before attempting this operation again."));
	remove_android_build_template->set_ok_button_text(TTR("Show in File Manager"));
	remove_android_build_template->connect("confirmed", callable_mp(this, &EditorNode::_menu_option).bind(FILE_EXPLORE_ANDROID_BUILD_TEMPLATES));
	gui_base->add_child(remove_android_build_template);
	file_templates = memnew(EditorFileDialog);
	file_templates->set_title(TTR("Import Templates From ZIP File"));
	gui_base->add_child(file_templates);
	file_templates->set_file_mode(EditorFileDialog::FILE_MODE_OPEN_FILE);
	file_templates->set_access(EditorFileDialog::ACCESS_FILESYSTEM);
	file_templates->clear_filters();
	file_templates->add_filter("*.tpz", TTR("Template Package"));
	file = memnew(EditorFileDialog);
	gui_base->add_child(file);
	file->set_current_dir("res:");
	file_export_lib = memnew(EditorFileDialog);
	file_export_lib->set_title(TTR("Export Library"));
	file_export_lib->set_file_mode(EditorFileDialog::FILE_MODE_SAVE_FILE);
	file_export_lib->connect("file_selected", callable_mp(this, &EditorNode::_dialog_action));
	file_export_lib_merge = memnew(CheckBox);
	file_export_lib_merge->set_text(TTR("Merge With Existing"));
	file_export_lib_merge->set_h_size_flags(Control::SIZE_SHRINK_CENTER);
	file_export_lib_merge->set_pressed(true);
	file_export_lib->get_vbox()->add_child(file_export_lib_merge);
	file_export_lib_apply_xforms = memnew(CheckBox);
	file_export_lib_apply_xforms->set_text(TTR("Apply MeshInstance Transforms"));
	file_export_lib_apply_xforms->set_h_size_flags(Control::SIZE_SHRINK_CENTER);
	file_export_lib_apply_xforms->set_pressed(false);