Thanks for the post and for bringing this to our attention!
I believe that essentially, you'll want to protect yourself the same way a brick-and-mortar store would. This includes printed/physical receipts and signatures, as in the event of a charge-back, you would have very compelling evidence to suggest the transaction was legitimate.
I found a helpful third-party resource here, which supports my recommendations above. As far as Shopify related content on chargebacks, we do have this comprehensive guide that discusses fraud that is specific to retail. The section on keeping accurate records and clearly defined store policies is especially important to note.
I will be sure to put in a request for more content and resources specific to scenarios that involve store pick-up and will post a reply when I have any relevant updates for you.
If I can help in any other way, please let me know.