### 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)

while (true) {
		assign = Variant();
		next_tag.fields.clear();
		next_tag.name = String();
		err = VariantParser::parse_tag_assign_eof(&stream, lines, error_text, next_tag, assign, value, nullptr, true);
		if (err == ERR_FILE_EOF) {
			
			
			_convert_to_last_version(config_version);
			last_save_time = FileAccess::get_modified_time(get_resource_path().path_join("project.godot"));
			return OK;
		}
		ERR_FAIL_COND_V_MSG(err != OK, err, "Error parsing " + p_path + " at line " + itos(lines) + ": " + error_text + " File might be corrupted.");
		if (!assign.is_empty()) {
			if (section.is_empty() && assign == "config_version") {
				config_version = value;
				ERR_FAIL_COND_V_MSG(config_version > CONFIG_VERSION, ERR_FILE_CANT_OPEN, vformat("Can't open project at '%s', its `config_version` (%d) is from a more recent and incompatible version of the engine. Expected config version: %d.", p_path, config_version, CONFIG_VERSION));
			} else {
				if (section.is_empty()) {
					set(assign, value);
				} else {
					set(section + "/" + assign, value);
				}
			}
		} else if (!next_tag.name.is_empty()) {
			section = next_tag.name;
		}
	}
}
Error ProjectSettings::_load_settings_text_or_binary(const String &p_text_path, const String &p_bin_path) {