You should be able to do it, but you need to add custom code to process the submitted data. You should be able to process it when the order is created by using the update_field() function to update the order custom fields.
If you only use it for WooCommerce, I suggest you use another plugin that is designed for that kind of situation. But if you need it for other things too, I recommend ACF.
I hope this helps 🙂
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