### 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)

const String res_path = resource_path.path_join("");
		
		
		cwd = cwd.path_join("");
		if (!cwd.begins_with(res_path)) {
			return p_path;
		}
		return cwd.replace_first(res_path, "res://");
	} else {
		int sep = path.rfind("/");
		if (sep == -1) {
			return "res://" + path;
		}
		String parent = path.substr(0, sep);
		String plocal = localize_path(parent);
		if (plocal.is_empty()) {
			return "";
		}
		
		if (plocal[plocal.length() - 1] == '/') {
			sep += 1;
		}
		return plocal + path.substr(sep, path.size() - sep);
	}
}
void ProjectSettings::set_initial_value(const String &p_name, const Variant &p_value) {