The vulnerability is only for a specific circumstance that you have to have opted into, which reduced the security level anyway. Probably the only people who would have done this are those using the Underground daily and don't want to have to unlock the phone when they want to tap in / out. This is no less vulnerable that having your contactless card outside of an RFID blocking wallet (which is most people). The issue is that they can go above the limit of contactless.
Just remove the travel express opt in and the vulnerability is gone. Apple Pay, Samsung Pay and Google Pay are all more secure than using contactless provided you don't use this feature on Apple Pay. It isn't the reason some banks are changing from Visa to Mastercard.
Some banks do also allow you to switch off functions of debit / credit cards. For example with Starling you can switch off contactless, the ability to swipe, to use in a cashpoint, use online etc within the app pretty much instantly. If you are totally paranoid then this is a good option for you.