### 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.
scene_tabs_context_menu->reset_size();
			scene_tabs_context_menu->add_shortcut(ED_GET_SHORTCUT("editor/new_scene"), FILE_NEW_SCENE);
			if (scene_tabs->get_hovered_tab() >= 0) {
				scene_tabs_context_menu->add_shortcut(ED_GET_SHORTCUT("editor/save_scene"), FILE_SAVE_SCENE);
				scene_tabs_context_menu->add_shortcut(ED_GET_SHORTCUT("editor/save_scene_as"), FILE_SAVE_AS_SCENE);
			}
			scene_tabs_context_menu->add_shortcut(ED_GET_SHORTCUT("editor/save_all_scenes"), FILE_SAVE_ALL_SCENES);
			if (scene_tabs->get_hovered_tab() >= 0) {
				scene_tabs_context_menu->add_separator();
				scene_tabs_context_menu->add_item(TTR("Show in FileSystem"), FILE_SHOW_IN_FILESYSTEM);
				scene_tabs_context_menu->add_item(TTR("Play This Scene"), FILE_RUN_SCENE);
				scene_tabs_context_menu->add_separator();
				scene_tabs_context_menu->add_shortcut(ED_GET_SHORTCUT("editor/close_scene"), FILE_CLOSE);
				scene_tabs_context_menu->set_item_text(scene_tabs_context_menu->get_item_index(FILE_CLOSE), TTR("Close Tab"));
				scene_tabs_context_menu->add_shortcut(ED_GET_SHORTCUT("editor/reopen_closed_scene"), FILE_OPEN_PREV);
				scene_tabs_context_menu->set_item_text(scene_tabs_context_menu->get_item_index(FILE_OPEN_PREV), TTR("Undo Close Tab"));
				if (previous_scenes.is_empty()) {
					scene_tabs_context_menu->set_item_disabled(scene_tabs_context_menu->get_item_index(FILE_OPEN_PREV), true);
				}
				scene_tabs_context_menu->add_item(TTR("Close Other Tabs"), FILE_CLOSE_OTHERS);
				scene_tabs_context_menu->add_item(TTR("Close Tabs to the Right"), FILE_CLOSE_RIGHT);
				scene_tabs_context_menu->add_item(TTR("Close All Tabs"), FILE_CLOSE_ALL);
			}
			scene_tabs_context_menu->set_position(scene_tabs->get_screen_position() + mb->get_position());
			scene_tabs_context_menu->reset_size();
			scene_tabs_context_menu->popup();
		}
	}
}
void EditorNode::_reposition_active_tab(int idx_to) {