### 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.
} else if (ED_IS_SHORTCUT("editor/editor_prev", p_event)) {
			_editor_select_prev();
		} else if (ED_IS_SHORTCUT("editor/command_palette", p_event)) {
			_open_command_palette();
		} else {
		}
		if (old_editor != editor_plugin_screen) {
			get_tree()->get_root()->set_input_as_handled();
		}
	}
}
void EditorNode::_update_from_settings() {
	int current_filter = GLOBAL_GET("rendering/textures/canvas_textures/default_texture_filter");
	if (current_filter != scene_root->get_default_canvas_item_texture_filter()) {
		Viewport::DefaultCanvasItemTextureFilter tf = (Viewport::DefaultCanvasItemTextureFilter)current_filter;
		scene_root->set_default_canvas_item_texture_filter(tf);
	}
	int current_repeat = GLOBAL_GET("rendering/textures/canvas_textures/default_texture_repeat");
	if (current_repeat != scene_root->get_default_canvas_item_texture_repeat()) {
		Viewport::DefaultCanvasItemTextureRepeat tr = (Viewport::DefaultCanvasItemTextureRepeat)current_repeat;
		scene_root->set_default_canvas_item_texture_repeat(tr);
	}
	RS::DOFBokehShape dof_shape = RS::DOFBokehShape(int(GLOBAL_GET("rendering/camera/depth_of_field/depth_of_field_bokeh_shape")));
	RS::get_singleton()->camera_attributes_set_dof_blur_bokeh_shape(dof_shape);
	RS::DOFBlurQuality dof_quality = RS::DOFBlurQuality(int(GLOBAL_GET("rendering/camera/depth_of_field/depth_of_field_bokeh_quality")));
	bool dof_jitter = GLOBAL_GET("rendering/camera/depth_of_field/depth_of_field_use_jitter");
	RS::get_singleton()->camera_attributes_set_dof_blur_quality(dof_quality, dof_jitter);
	RS::get_singleton()->environment_set_ssao_quality(RS::EnvironmentSSAOQuality(int(GLOBAL_GET("rendering/environment/ssao/quality"))), GLOBAL_GET("rendering/environment/ssao/half_size"), GLOBAL_GET("rendering/environment/ssao/adaptive_target"), GLOBAL_GET("rendering/environment/ssao/blur_passes"), GLOBAL_GET("rendering/environment/ssao/fadeout_from"), GLOBAL_GET("rendering/environment/ssao/fadeout_to"));
	RS::get_singleton()->screen_space_roughness_limiter_set_active(GLOBAL_GET("rendering/anti_aliasing/screen_space_roughness_limiter/enabled"), GLOBAL_GET("rendering/anti_aliasing/screen_space_roughness_limiter/amount"), GLOBAL_GET("rendering/anti_aliasing/screen_space_roughness_limiter/limit"));
	bool glow_bicubic = int(GLOBAL_GET("rendering/environment/glow/upscale_mode")) > 0;