The only situation I can envisage this happening is (as has happened to me a couple of times) when the biometrics fall out of the system. Of course the first time this occurred was when flying a wholly domestic itinerary (actually this was Newcastle!) when I chose not take my passport with me. The gate agent called G4S security who came to talk to me and look at my passport(!), asked a few questions about where I'd travelled from. Fortunately I had my UK Driving Licence (which shows me as being born in the UK) and I was good to go, although I was the very last to board.

My only concern for the OP's friend is how he could he establish his right of residence in the UK should his biometrics fall out of the system? Perhaps as a precaution he could carry a photocopy of his passport, or take his biometric residence permit or a letter from the Home Office with his immigration reference number included together with his driving licence?

Even if he cannot produce any of those documents, an Immigration Officer would be called and they could verify his immigration status by taking his fingerprint or from questioning about his immigration history. If an interview with an Immigration Officer becomes necessary, that could cause him to miss his flight (although in those circumstances I'd expect the airline to re-accommodate him FOC).