We can not prevent Apple Pay popups from SDK but you can contact Apple to provide special entitlement for you app to prevent it while app is in foreground. More information: https://developer.apple.com/documentation/passkit/pkpasslibrary/1617078-requestautomaticpasspresentation
Core NFC
SDK is not implemented with Core NFC, we use only BLE inside SDK but locks do support NFC and that triggers Apple Pay popup. Unfortunately there is no way around it since you need to trigger lock before sending mobile key via BLE. We would suggest you to record video of lock opening and showing Apple Pay popup and send that to Apple.
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