Yep, if you don't pay through the normal Instant Pay link it gives you, there is no way for it to know.
If I remember right, it was not working well back then. It was working for some transactions and not others. I remember the $65 auction in particular. The seller wanted his money quickly but also was very intent on getting the feedback score. We went round and around trying to get the payment through the system. Would be nice if the system allowed me to comment on the transactions in question. It's like they count enough to be part of my score but not enough to allow for feedback/comments. Perhaps then I could find the seller and get them to comment that I did in fact pay them.