### 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)

} else {
		file->store_32(count); 
	}
	for (const KeyValue<String, List<String>> &E : p_props) {
		for (const String &key : E.value) {
			String k = key;
			if (!E.key.is_empty()) {
				k = E.key + "/" + k;
			}
			Variant value;
			if (p_custom.has(k)) {
				value = p_custom[k];
			} else {
				value = get(k);
			}
			file->store_pascal_string(k);
			int len;
			err = encode_variant(value, nullptr, len, true);
			ERR_FAIL_COND_V_MSG(err != OK, ERR_INVALID_DATA, "Error when trying to encode Variant.");
			Vector<uint8_t> buff;
			buff.resize(len);
			err = encode_variant(value, buff.ptrw(), len, true);
			ERR_FAIL_COND_V_MSG(err != OK, ERR_INVALID_DATA, "Error when trying to encode Variant.");
			file->store_32(len);
			file->store_buffer(buff.ptr(), buff.size());
		}
	}
	return OK;
}
Error ProjectSettings::_save_settings_text(const String &p_file, const RBMap<String, List<String>> &p_props, const CustomMap &p_custom, const String &p_custom_features) {