Customarily, you would want to use Transaction ID, as that refers to a specific completed payment with the payment processor (PayPal/etc.), so it serves as a receipt number or "proof of purchase" which you or the buyer can look up in your payment processor account. The Invoice ID is another, much longer string that the buyer might find in their payment history, so we log that for you as well in case they reference that instead of the Txn ID in their communications to you.
Because that Txn ID serves as proof of purchase and is used in your thank-you/download page URLs (and some sellers use it for other purposes requiring proof of purchase as well), we would not want to reveal that ID to any affiliate who might have referred the sale. Thus, affiliates are only shown the E-j Internal Txn ID (which is not logged anywhere at the payment processor's end) in their referred-sale Notifications and Earnings Report, so if they need to contact the seller regarding their commission on a specific sale, they have a reference number that cannot be used to impersonate the buyer or obtain the actual product.