Yes, PDF Stamping only works on downloads issued from an actual checkout, nor for links issued manually using "Send free download link." To handle buyers who pay by other means, you can create a secret discount code that you can use to place an online order for free on the buyer's behalf.
To issue a link in this manner, you'd go to your site, Add to Cart your item, enter your secret discount code to reduce the order total to 0.00, then proceed to Free Checkout where you'd enter the buyer's name and email address. They would receive a thank-you email with a link to download their file, which would be stamped with the name/email that you'd provided in that Free Checkout and the Transaction ID for that online order.
