### 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)

_THREAD_SAFE_METHOD_
	StringName name = p_name;
	if (feature_overrides.has(name)) {
		const LocalVector<Pair<StringName, StringName>> &overrides = feature_overrides[name];
		for (uint32_t i = 0; i < overrides.size(); i++) {
			if (OS::get_singleton()->has_feature(overrides[i].first)) { 
				if (props.has(overrides[i].second)) {
					name = overrides[i].second;
					break;
				}
			}
		}
	}
	if (!props.has(name)) {
		WARN_PRINT("Property not found: " + String(name));
		return Variant();
	}
	return props[name].variant;
}
struct _VCSort {
	String name;
	Variant::Type type = Variant::VARIANT_MAX;
	int order = 0;
	uint32_t flags = 0;
	bool operator<(const _VCSort &p_vcs) const { return order == p_vcs.order ? name < p_vcs.name : order < p_vcs.order; }