It could be like the Australian (and presumably, New Zealand) ETA: United's computer checks to see if there's an Australian ETA associated with the passport number, but check-in and gate agents can override a failed online check-in.

Just last month, I couldn't check in for my SFO-BNE through the app. I went to the airport to use the check-in kiosk and failed to get a boarding pass. Someone came over, walked me over to one of the check-in desks and asked me for my Australian ETA email and passport. She confirmed the Australian ETA email hadn't expired, matched my passport number and the passport number matched what I used to try to check in. She then input the ETA's valid-until date from the email into the computer to check me in and print my boarding pass.