### 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.
RS::get_singleton()->environment_set_ssil_quality(RS::EnvironmentSSILQuality(int(GLOBAL_GET("rendering/environment/ssil/quality"))), GLOBAL_GET("rendering/environment/ssil/half_size"), GLOBAL_GET("rendering/environment/ssil/adaptive_target"), GLOBAL_GET("rendering/environment/ssil/blur_passes"), GLOBAL_GET("rendering/environment/ssil/fadeout_from"), GLOBAL_GET("rendering/environment/ssil/fadeout_to"));
	RS::get_singleton()->environment_glow_set_use_bicubic_upscale(glow_bicubic);
	RS::EnvironmentSSRRoughnessQuality ssr_roughness_quality = RS::EnvironmentSSRRoughnessQuality(int(GLOBAL_GET("rendering/environment/screen_space_reflection/roughness_quality")));
	RS::get_singleton()->environment_set_ssr_roughness_quality(ssr_roughness_quality);
	RS::SubSurfaceScatteringQuality sss_quality = RS::SubSurfaceScatteringQuality(int(GLOBAL_GET("rendering/environment/subsurface_scattering/subsurface_scattering_quality")));
	RS::get_singleton()->sub_surface_scattering_set_quality(sss_quality);
	float sss_scale = GLOBAL_GET("rendering/environment/subsurface_scattering/subsurface_scattering_scale");
	float sss_depth_scale = GLOBAL_GET("rendering/environment/subsurface_scattering/subsurface_scattering_depth_scale");
	RS::get_singleton()->sub_surface_scattering_set_scale(sss_scale, sss_depth_scale);
	uint32_t directional_shadow_size = GLOBAL_GET("rendering/lights_and_shadows/directional_shadow/size");
	uint32_t directional_shadow_16_bits = GLOBAL_GET("rendering/lights_and_shadows/directional_shadow/16_bits");
	RS::get_singleton()->directional_shadow_atlas_set_size(directional_shadow_size, directional_shadow_16_bits);
	RS::ShadowQuality shadows_quality = RS::ShadowQuality(int(GLOBAL_GET("rendering/lights_and_shadows/positional_shadow/soft_shadow_filter_quality")));
	RS::get_singleton()->positional_soft_shadow_filter_set_quality(shadows_quality);
	RS::ShadowQuality directional_shadow_quality = RS::ShadowQuality(int(GLOBAL_GET("rendering/lights_and_shadows/directional_shadow/soft_shadow_filter_quality")));
	RS::get_singleton()->directional_soft_shadow_filter_set_quality(directional_shadow_quality);
	float probe_update_speed = GLOBAL_GET("rendering/lightmapping/probe_capture/update_speed");
	RS::get_singleton()->lightmap_set_probe_capture_update_speed(probe_update_speed);
	RS::EnvironmentSDFGIFramesToConverge frames_to_converge = RS::EnvironmentSDFGIFramesToConverge(int(GLOBAL_GET("rendering/global_illumination/sdfgi/frames_to_converge")));
	RS::get_singleton()->environment_set_sdfgi_frames_to_converge(frames_to_converge);
	RS::EnvironmentSDFGIRayCount ray_count = RS::EnvironmentSDFGIRayCount(int(GLOBAL_GET("rendering/global_illumination/sdfgi/probe_ray_count")));
	RS::get_singleton()->environment_set_sdfgi_ray_count(ray_count);
	RS::VoxelGIQuality voxel_gi_quality = RS::VoxelGIQuality(int(GLOBAL_GET("rendering/global_illumination/voxel_gi/quality")));
	RS::get_singleton()->voxel_gi_set_quality(voxel_gi_quality);
	RS::get_singleton()->environment_set_volumetric_fog_volume_size(GLOBAL_GET("rendering/environment/volumetric_fog/volume_size"), GLOBAL_GET("rendering/environment/volumetric_fog/volume_depth"));
	RS::get_singleton()->environment_set_volumetric_fog_filter_active(bool(GLOBAL_GET("rendering/environment/volumetric_fog/use_filter")));
	RS::get_singleton()->canvas_set_shadow_texture_size(GLOBAL_GET("rendering/2d/shadow_atlas/size"));
	bool use_half_res_gi = GLOBAL_GET("rendering/global_illumination/gi/use_half_resolution");
	RS::get_singleton()->gi_set_use_half_resolution(use_half_res_gi);
	bool snap_2d_transforms = GLOBAL_GET("rendering/2d/snap/snap_2d_transforms_to_pixel");