Sounds to me like they were too timid. Once you comply with Timatic (and I always bring a printout with me when traveling to places with picky requirements), the airline should allow you to travel, and your friend should have demanded a supervisor and refused to leave the counter until their issue was escalated as far as it needed to be.

I had many a run-in with United check-in agents who refused to believe there was such a thing as the China TWOV program, and insisted on seeing my visa before checking me in - each of those interactions required me to demand a supervisor, and then demand they call their help desk to get trained on the rules. In both cases I was checked-in and flew, although I left some very unhappy counter agents in my wake.

You don't need to jump up and down and scream, but being firm and insisting on the correct resolution that you know is right is often an unfortunate side effect of poor airline employee training, and lazy agents.

I am glad I saw this post, however - just to avoid my own arguments, I've downloaded the app and will upload my vaccine record so there can be no dispute.