I believe these are all considered separate payment methods.
If you register your card on TFL website (contactless.tfl.gov.uk) and use the same card with Apple Pay you would see that TFL will automatically create another card on your account.
Reason for this is that Apple/Google Pay use virtual card numbers instead of the real card number.
I only added my Monzo card once but because I use Google Pay, TFL added the same card with a different reference;
