### 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)

if (v->variant == v->initial) {
				continue;
			}
			vclist.insert(vc);
		}
	}
	for (const KeyValue<String, Variant> &E : p_custom) {
		
		RBMap<StringName, VariantContainer>::Iterator global_prop = props.find(E.key);
		_VCSort vc;
		vc.name = E.key;
		vc.order = global_prop ? global_prop->value.order : 0xFFFFFFF;
		vc.type = E.value.get_type();
		vc.flags = PROPERTY_USAGE_STORAGE;
		vclist.insert(vc);
	}
	RBMap<String, List<String>> save_props;
	for (const _VCSort &E : vclist) {
		String category = E.name;
		String name = E.name;
		int div = category.find("/");
		if (div < 0) {
			category = "";
		} else {
			category = category.substr(0, div);
			name = name.substr(div + 1, name.size());
		}
		save_props[category].push_back(name);
	}
	String save_features;