### 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)

return singleton;
}
String ProjectSettings::get_project_data_dir_name() const {
	return project_data_dir_name;
}
String ProjectSettings::get_project_data_path() const {
	return "res://" + get_project_data_dir_name();
}
String ProjectSettings::get_resource_path() const {
	return resource_path;
}
String ProjectSettings::get_safe_project_name() const {
	String safe_name = OS::get_singleton()->get_safe_dir_name(get("application/config/name"));
	if (safe_name.is_empty()) {
		safe_name = "UnnamedProject";
	}
	return safe_name;
}
String ProjectSettings::get_imported_files_path() const {
	return get_project_data_path().path_join("imported");
}
#ifdef TOOLS_ENABLED
const PackedStringArray ProjectSettings::get_required_features() {