### 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.
help_menu->set_item_icon(help_menu->get_item_index(HELP_QA), gui_base->get_theme_icon(SNAME("ExternalLink"), SNAME("EditorIcons")));
			help_menu->set_item_icon(help_menu->get_item_index(HELP_REPORT_A_BUG), gui_base->get_theme_icon(SNAME("ExternalLink"), SNAME("EditorIcons")));
			help_menu->set_item_icon(help_menu->get_item_index(HELP_COPY_SYSTEM_INFO), gui_base->get_theme_icon(SNAME("ActionCopy"), SNAME("EditorIcons")));
			help_menu->set_item_icon(help_menu->get_item_index(HELP_SUGGEST_A_FEATURE), gui_base->get_theme_icon(SNAME("ExternalLink"), SNAME("EditorIcons")));
			help_menu->set_item_icon(help_menu->get_item_index(HELP_SEND_DOCS_FEEDBACK), gui_base->get_theme_icon(SNAME("ExternalLink"), SNAME("EditorIcons")));
			help_menu->set_item_icon(help_menu->get_item_index(HELP_COMMUNITY), gui_base->get_theme_icon(SNAME("ExternalLink"), SNAME("EditorIcons")));
			help_menu->set_item_icon(help_menu->get_item_index(HELP_ABOUT), gui_base->get_theme_icon(SNAME("Godot"), SNAME("EditorIcons")));
			help_menu->set_item_icon(help_menu->get_item_index(HELP_SUPPORT_GODOT_DEVELOPMENT), gui_base->get_theme_icon(SNAME("Heart"), SNAME("EditorIcons")));
			for (int i = 0; i < main_editor_buttons.size(); i++) {
				main_editor_buttons.write[i]->add_theme_font_override("font", gui_base->get_theme_font(SNAME("main_button_font"), SNAME("EditorFonts")));
				main_editor_buttons.write[i]->add_theme_font_size_override("font_size", gui_base->get_theme_font_size(SNAME("main_button_font_size"), SNAME("EditorFonts")));
			}
			HashSet<String> updated_textfile_extensions;
			bool extensions_match = true;
			const Vector<String> textfile_ext = ((String)(EDITOR_GET("docks/filesystem/textfile_extensions"))).split(",", false);
			for (const String &E : textfile_ext) {
				updated_textfile_extensions.insert(E);
				if (extensions_match && !textfile_extensions.has(E)) {
					extensions_match = false;
				}
			}
			if (!extensions_match || updated_textfile_extensions.size() < textfile_extensions.size()) {
				textfile_extensions = updated_textfile_extensions;
				EditorFileSystem::get_singleton()->scan();
			}
			_update_update_spinner();
		} break;
	}
}
void EditorNode::_update_update_spinner() {