### 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)

};
void ProjectSettings::_get_property_list(List<PropertyInfo> *p_list) const {
	_THREAD_SAFE_METHOD_
	RBSet<_VCSort> vclist;
	for (const KeyValue<StringName, VariantContainer> &E : props) {
		const VariantContainer *v = &E.value;
		if (v->hide_from_editor) {
			continue;
		}
		_VCSort vc;
		vc.name = E.key;
		vc.order = v->order;
		vc.type = v->variant.get_type();
		if (v->internal || vc.name.begins_with("input/") || vc.name.begins_with("importer_defaults/") || vc.name.begins_with("import/") || vc.name.begins_with("autoload/") || vc.name.begins_with("editor_plugins/") || vc.name.begins_with("shader_globals/")) {
			vc.flags = PROPERTY_USAGE_STORAGE;
		} else {