Went to Australia last year with Cathay from London. Left it to the travel agent to sort out the visas which he duly did. Turned up at the Cathay check in deck to be told my visa was ok but wife's was not. Apparently two digits were reversed on her visa and the 'computer says no', not that we saw any paperwork at any time and the check in lady was staring at a computer screen. She made a phone call, spoke a few sentences then handed us back our passports and said all sorted, there you go.
I asked her what would have happened if she had not been able to sort it out, she pointed to the ticket sales desk and said I would have just sent you over there and they would have sorted it out. I really got the impression it was no big deal. I don't mean no big deal about not having a visa, I mean no big deal getting one sorted.
I guess this would allow for late ticket sales etc, otherwise how would last minute changes or ticket purchases be dealt with?