### 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)

PackedStringArray features = PackedStringArray(p_project_features);
	PackedStringArray supported_features = _get_supported_features();
	for (int i = p_project_features.size() - 1; i > -1; i--) {
		if (!supported_features.has(p_project_features[i])) {
			features.remove_at(i);
		}
	}
	
	PackedStringArray required_features = get_required_features();
	for (int i = 0; i < required_features.size(); i++) {
		if (!features.has(required_features[i])) {
			features.append(required_features[i]);
		}
	}
	features.sort();
	return features;
}
#endif 
String ProjectSettings::localize_path(const String &p_path) const {