Blue Eagle,
you’re right – it is quite pathetic, but it happened a couple of years ago: The situation: Biz-class cat (4 legs) in leakproof container of correct size, plenty of empty seats, so ALL of the prescribed conditions(!) were met. Small biz-class (3 rows) – one of the other biz-pax brought the allergy-issue to the attention of the F/A – he notified the commander, who ignored this and departed anyway. Guess what – allergic reaction – pax had to be reseated to last row (eco, of course) – a LOT of legal conversation and paperwork. The commander was cautioned for NOT “varying the limitations”, this time the other way round (!!!). By the way, nobody ever cared about whether this “allergy” was real or caused by that specific cat… - THAT's reality!
Just the fact that someone was accepted for travel by the airline and made it onto the plane does not relieve the crew from its responsibility to ascertain a safe flight. Moreover, if anything unusual is brought to the attention of the commander, he/she is legally expected to use his/her quite far-reaching authority to make a decision always in favour of safety – even beyond company-standards.