### 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)

Error err = _setup(p_path, p_main_pack, p_upwards, p_ignore_override);
	if (err == OK) {
		String custom_settings = GLOBAL_GET("application/config/project_settings_override");
		if (!custom_settings.is_empty()) {
			_load_settings_text(custom_settings);
		}
	}
	
	bool use_hidden_directory = GLOBAL_GET("application/config/use_hidden_project_data_directory");
	project_data_dir_name = (use_hidden_directory ? "." : "") + PROJECT_DATA_DIR_NAME_SUFFIX;
	
	Compression::zstd_long_distance_matching = GLOBAL_GET("compression/formats/zstd/long_distance_matching");
	Compression::zstd_level = GLOBAL_GET("compression/formats/zstd/compression_level");
	Compression::zstd_window_log_size = GLOBAL_GET("compression/formats/zstd/window_log_size");
	Compression::zlib_level = GLOBAL_GET("compression/formats/zlib/compression_level");
	Compression::gzip_level = GLOBAL_GET("compression/formats/gzip/compression_level");
	project_loaded = err == OK;
	return err;
}
bool ProjectSettings::has_setting(String p_var) const {
	_THREAD_SAFE_METHOD_
	return props.has(p_var);
}
Error ProjectSettings::_load_settings_binary(const String &p_path) {