### 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 (InputMap::get_singleton()) {
		HashMap<String, List<Ref<InputEvent>>> builtins = InputMap::get_singleton()->get_builtins();
		for (KeyValue<String, List<Ref<InputEvent>>> &E : builtins) {
			Array events;
			
			for (List<Ref<InputEvent>>::Element *I = E.value.front(); I; I = I->next()) {
				events.push_back(I->get());
			}
			Dictionary action;
			action["deadzone"] = Variant(0.5f);
			action["events"] = events;
			String action_name = "input/" + E.key;
			GLOBAL_DEF(action_name, action);
			input_presets.push_back(action_name);
		}
	}
}
ProjectSettings::ProjectSettings() {
	
	
	CRASH_COND_MSG(singleton != nullptr, "Instantiating a new ProjectSettings singleton is not supported.");
	singleton = this;
	GLOBAL_DEF_BASIC("application/config/name", "");