### 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)

return get_project_data_path().path_join("global_script_class_cache.cfg");
}
void ProjectSettings::store_global_class_list(const Array &p_classes) {
	Ref<ConfigFile> cf;
	cf.instantiate();
	cf->set_value("", "list", p_classes);
	cf->save(get_global_class_list_path());
	global_class_list = p_classes;
}
bool ProjectSettings::has_custom_feature(const String &p_feature) const {
	return custom_features.has(p_feature);
}
const HashMap<StringName, ProjectSettings::AutoloadInfo> &ProjectSettings::get_autoload_list() const {
	return autoloads;
}
void ProjectSettings::add_autoload(const AutoloadInfo &p_autoload) {
	ERR_FAIL_COND_MSG(p_autoload.name == StringName(), "Trying to add autoload with no name.");
	autoloads[p_autoload.name] = p_autoload;
}
void ProjectSettings::remove_autoload(const StringName &p_autoload) {
	ERR_FAIL_COND_MSG(!autoloads.has(p_autoload), "Trying to remove non-existent autoload.");
	autoloads.erase(p_autoload);
}
bool ProjectSettings::has_autoload(const StringName &p_autoload) const {