First, I would have thought you would be able to make a Bluetooth connection without getting close enough for the NFC to be detected, but that isn't your question.
You can suppress the ApplePay display when your app is in the foreground by calling requestAutomaticPassPresentationSuppression(responseHandler:)
from the PassKit framework.
Note that:
This method requires a special entitlement issued by Apple. If the entitlement is not present, the request will fail with a PKPassLibrary result.
Specifically, you need the com.apple.developer.passkit.pass-presentation-suppression
entitlement.
If this app is for your own use you should be able to just add this entitlement to your entitlements file. To submit it to the App Store you will need to contact Apple to get this entitlement.
You cannot suppress ApplePay when your app is not in the foreground.