### 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)

value = p_custom[key];
			} else {
				value = get(key);
			}
			String vstr;
			VariantWriter::write_to_string(value, vstr);
			file->store_string(F.property_name_encode() + "=" + vstr + "\n");
		}
	}
	return OK;
}
Error ProjectSettings::_save_custom_bnd(const String &p_file) { 
	return save_custom(p_file);
}
Error ProjectSettings::save_custom(const String &p_path, const CustomMap &p_custom, const Vector<String> &p_custom_features, bool p_merge_with_current) {
	ERR_FAIL_COND_V_MSG(p_path.is_empty(), ERR_INVALID_PARAMETER, "Project settings save path cannot be empty.");
#ifdef TOOLS_ENABLED
	PackedStringArray project_features = get_setting("application/config/features");
	
	if (project_features.is_empty()) {
		project_features = ProjectSettings::get_required_features();
	}
	
	const String rendering_api = has_setting("rendering/renderer/rendering_method") ? (String)get_setting("rendering/renderer/rendering_method") : String();
	if (!rendering_api.is_empty()) {
		
		if (!project_features.has(rendering_api)) {
			project_features.append(rendering_api);
		}
	}