### 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.
bool is_resource = current_obj->is_class("Resource");
	bool is_node = current_obj->is_class("Node");
	bool stay_in_script_editor_on_node_selected = bool(EDITOR_GET("text_editor/behavior/navigation/stay_in_script_editor_on_node_selected"));
	bool skip_main_plugin = false;
	String editable_info; 
	bool info_is_warning = false;
	if (current_obj->has_method("_is_read_only")) {
		if (current_obj->call("_is_read_only")) {
			editable_info = TTR("This object is marked as read-only, so it's not editable.");
		}
	}
	if (is_resource) {
		Resource *current_res = Object::cast_to<Resource>(current_obj);
		ERR_FAIL_COND(!current_res);
		InspectorDock::get_inspector_singleton()->edit(current_res);
		SceneTreeDock::get_singleton()->set_selected(nullptr);
		NodeDock::get_singleton()->set_node(nullptr);
		InspectorDock::get_singleton()->update(nullptr);
		ImportDock::get_singleton()->set_edit_path(current_res->get_path());
		int subr_idx = current_res->get_path().find("::");
		if (subr_idx != -1) {
			String base_path = current_res->get_path().substr(0, subr_idx);
			if (!base_path.is_resource_file()) {
				if (FileAccess::exists(base_path + ".import")) {
					if (get_edited_scene() && get_edited_scene()->get_scene_file_path() == base_path) {
						info_is_warning = true;
					}
					editable_info = TTR("This resource belongs to a scene that was imported, so it's not editable.\nPlease read the documentation relevant to importing scenes to better understand this workflow.");
				} else {
					if ((!get_edited_scene() || get_edited_scene()->get_scene_file_path() != base_path) && ResourceLoader::get_resource_type(base_path) == "PackedScene") {