WooCommerce is a great platform for creating unique and interesting stores. Unfortunately, the flexibility of WooCommerce means there's no way to automate adding gift messages to orders that come through to a linked Inkthreadable account.
But that doesn't mean you can't add gift messages to WooCommerce orders; you simply add them manually instead. You can read about how to do this here.
Please note: if a gift message is included on a packing slip the resale price is not shown by default.