### 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.
vbc->add_child(disk_changed_list);
		disk_changed_list->set_v_size_flags(Control::SIZE_EXPAND_FILL);
		disk_changed->connect("confirmed", callable_mp(this, &EditorNode::_reload_modified_scenes));
		disk_changed->connect("confirmed", callable_mp(this, &EditorNode::_reload_project_settings));
		disk_changed->set_ok_button_text(TTR("Reload"));
		disk_changed->add_button(TTR("Resave"), !DisplayServer::get_singleton()->get_swap_cancel_ok(), "resave");
		disk_changed->connect("custom_action", callable_mp(this, &EditorNode::_resave_scenes));
	}
	gui_base->add_child(disk_changed);
	add_editor_plugin(memnew(AnimationPlayerEditorPlugin));
	add_editor_plugin(memnew(AnimationTrackKeyEditEditorPlugin));
	add_editor_plugin(memnew(CanvasItemEditorPlugin));
	add_editor_plugin(memnew(Node3DEditorPlugin));
	add_editor_plugin(memnew(ScriptEditorPlugin));
	EditorAudioBuses *audio_bus_editor = EditorAudioBuses::register_editor();
	ScriptTextEditor::register_editor(); 
	TextEditor::register_editor();
	if (AssetLibraryEditorPlugin::is_available()) {
		add_editor_plugin(memnew(AssetLibraryEditorPlugin));
	} else {
		print_verbose("Asset Library not available (due to using Web editor, or SSL support disabled).");
	}
	
	raise_bottom_panel_item(AnimationPlayerEditor::get_singleton());
	add_editor_plugin(VersionControlEditorPlugin::get_singleton());
	vcs_actions_menu = VersionControlEditorPlugin::get_singleton()->get_version_control_actions_panel();
	vcs_actions_menu->set_name("Version Control");
	vcs_actions_menu->connect("index_pressed", callable_mp(this, &EditorNode::_version_control_menu_option));
	vcs_actions_menu->add_item(TTR("Create Version Control Metadata"), RUN_VCS_METADATA);
	vcs_actions_menu->add_item(TTR("Version Control Settings"), RUN_VCS_SETTINGS);