### 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)

resource_path = current_dir;
		resource_path = resource_path.replace("\\", "/"); 
		err = _load_settings_text_or_binary(current_dir.path_join("project.godot"), current_dir.path_join("project.binary"));
		if (err == OK && !p_ignore_override) {
			
			_load_settings_text(current_dir.path_join("override.cfg"));
			found = true;
			break;
		}
		if (p_upwards) {
			
			d->change_dir("..");
			if (d->get_current_dir() == current_dir) {
				break; 
			}
			current_dir = d->get_current_dir();
		} else {
			break;
		}
	}
	if (!found) {
		return err;
	}
	if (resource_path.length() && resource_path[resource_path.length() - 1] == '/') {
		resource_path = resource_path.substr(0, resource_path.length() - 1); 
	}
	return OK;
}
Error ProjectSettings::setup(const String &p_path, const String &p_main_pack, bool p_upwards, bool p_ignore_override) {