### 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.
if (in_use) {
			vsplits[i]->show();
		} else {
			vsplits[i]->hide();
		}
	}
	if (right_l_vsplit->is_visible() || right_r_vsplit->is_visible()) {
		right_hsplit->show();
	} else {
		right_hsplit->hide();
	}
	for (int i = 0; i < DOCK_SLOT_MAX; i++) {
		if (dock_slot[i]->is_visible() && dock_slot[i]->get_tab_count()) {
			dock_slot[i]->set_current_tab(0);
		}
	}
	
	if (p_layout->has_section_key(p_section, "dock_filesystem_split")) {
		int fs_split_ofs = p_layout->get_value(p_section, "dock_filesystem_split");
		FileSystemDock::get_singleton()->set_split_offset(fs_split_ofs);
	}
	if (p_layout->has_section_key(p_section, "dock_filesystem_display_mode")) {
		FileSystemDock::DisplayMode dock_filesystem_display_mode = FileSystemDock::DisplayMode(int(p_layout->get_value(p_section, "dock_filesystem_display_mode")));
		FileSystemDock::get_singleton()->set_display_mode(dock_filesystem_display_mode);
	}
	if (p_layout->has_section_key(p_section, "dock_filesystem_file_sort")) {
		FileSystemDock::FileSortOption dock_filesystem_file_sort = FileSystemDock::FileSortOption(int(p_layout->get_value(p_section, "dock_filesystem_file_sort")));
		FileSystemDock::get_singleton()->set_file_sort(dock_filesystem_file_sort);
	}
	if (p_layout->has_section_key(p_section, "dock_filesystem_file_list_display_mode")) {