### 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)

bool found = _load_resource_pack(exec_path);
		
		
		String exec_dir = exec_path.get_base_dir();
		String exec_filename = exec_path.get_file();
		String exec_basename = exec_filename.get_basename();
		
		
		
		
#ifdef MACOS_ENABLED
		if (!found) {
			
			found = _load_resource_pack(OS::get_singleton()->get_bundle_resource_dir().path_join(exec_basename + ".pck")) || _load_resource_pack(OS::get_singleton()->get_bundle_resource_dir().path_join(exec_filename + ".pck"));
		}
#endif
		if (!found) {
			
			
			found = _load_resource_pack(exec_dir.path_join(exec_basename + ".pck")) || _load_resource_pack(exec_dir.path_join(exec_filename + ".pck"));
		}
		if (!found) {
			
			
			found = _load_resource_pack(exec_basename + ".pck") || _load_resource_pack(exec_filename + ".pck");
		}