I’ve used my phone and ApplePay (with my bank’s credit card) in many stores where the staff said it wouldn’t work. Works fine.
The only places I’ve been to where my phone doesn’t work are places where tapping the physical card doesn’t work either.
If it is possible to block ApplePay without blocking contactless cards in general, I haven’t ever seen it in action (in the Washington DC metro area). All the stores I’ve been to that block one also block the other.