A merchant can't match an Apple Pay payment to your bank card. They don't receive your bank card details when you pay by Apple Pay, but rather the Device Account Number which is generated when you set up the card in Apple Pay.
What they, apparantely, will be able to do is scan your phone with their handheld device in the same way that they scan a contactless bank card. This will be just as effective as a contactless card in verifying that you've paid.
This does mean that you need to be careful not to mix Apple Pay and contactless card payments, or you could end up paying more. The automatic daily and weekly fare capping, for example, relies on you using the same payment method for all your journeys.
And if you were to "touch in" with Apple Pay and then "touch out" with a bank card, you'd end up paying 2 fares (and they would both be expensive "incomplete journey" fares).