### 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)

Pair<StringName, StringName> feature_override(feature, p_name);
					if (!feature_overrides.has(s[0])) {
						feature_overrides[s[0]] = LocalVector<Pair<StringName, StringName>>();
					}
					feature_overrides[s[0]].push_back(feature_override);
				}
			}
		}
		if (props.has(p_name)) {
			props[p_name].variant = p_value;
		} else {
			props[p_name] = VariantContainer(p_value, last_order++);
		}
		if (p_name.operator String().begins_with("autoload/")) {
			String node_name = p_name.operator String().split("/")[1];
			AutoloadInfo autoload;
			autoload.name = node_name;
			String path = p_value;
			if (path.begins_with("*")) {
				autoload.is_singleton = true;
				autoload.path = path.substr(1);
			} else {
				autoload.path = path;
			}
			add_autoload(autoload);
		}
	}
	return true;
}
bool ProjectSettings::_get(const StringName &p_name, Variant &r_ret) const {