### Godot version

v4.0.beta10.official [d0398f62f]

### System information

Windows 11

### Issue description

Using a custom "Project Settings Override" file causes Godot to immediately modify main project file (`.godot`) on startup.

The attached project demonstrates this issue. The project has the following 3 things defined:

1. Window display mode is set to "Exclusive Fullscreen" (`window/size/mode=4`) in main project file.
2. Custom project override file is set to "res://override.cfg" (`config/project_settings_override`).
3. Inside "res://override.cfg" window display mode is set to "Windowed" (`window/size/mode=0`).

Opening this project will immediately modify main project file to have "Windowed" display mode (discarding original "Exclusive Fullscreen" setting).

### Steps to reproduce

1. Open example project.
2. Go to Project Settings -> Display -> Window -> Mode.
3. Expected option is "Exclusive Fullscreen", actual result is "Windowed".

### Minimal reproduction project

[override-issue.zip](https://github.com/godotengine/godot/files/10312624/override-issue.zip)

if (found) {
			Error err = _load_settings_text_or_binary("res://project.godot", "res://project.binary");
			if (err == OK && !p_ignore_override) {
				
				
				_load_settings_text("res://override.cfg");
				_load_settings_text(exec_path.get_base_dir().path_join("override.cfg"));
			}
			return err;
		}
	}
	
	
	if (!OS::get_singleton()->get_resource_dir().is_empty()) {
		Error err = _load_settings_text_or_binary("res://project.godot", "res://project.binary");
		if (err == OK && !p_ignore_override) {
			
			_load_settings_text("res://override.cfg");
		}
		return err;
	}
	
	
	Ref<DirAccess> d = DirAccess::create(DirAccess::ACCESS_FILESYSTEM);
	ERR_FAIL_COND_V_MSG(d.is_null(), ERR_CANT_CREATE, "Cannot create DirAccess for path '" + p_path + "'.");
	d->change_dir(p_path);
	String current_dir = d->get_current_dir();
	bool found = false;
	Error err;
	while (true) {