FaceID as government ID is not a good idea, and it’s fine to start somewhere in my opinion though of course I would prefer outlawing biometrics entirely as identifiers.
This is both in the precheck security line and when boarding international flights.
It was an issue once with a Delta employee who didn’t know I could opt out. And once with border control in Ireland (where ICE has a presence). There, the ICE employee manually verified me but still insisted I get a photo taken.
Otherwise, it’s not been an issue to opt out so far. The staff might be a little annoyed, but it goes just as fast.
That being said, did your airport not have signs talking about the pilot, and it being optional? I would of pointed to that if I was told no.