Yeah, I don't like your trainer's answer either.
Dogs growl because they are uncomfortable. It is a polite way of asking for space, and I'm very glad you responded by immediately pulling Pax out of a situation that, for whatever reason, wasn't working for him. It's fairly likely that he was signaling some discomfort before he growled, but so subtly that no one noticed (or mistook it for pleasure at having his rump scratched -- freezing, pulling ears back, etc. could probably be mistaken for several things). Learning to watch for the subtler signs would probably be good, so that you can intervene faster. Listening to your dog is important for trust as well as safety...I think you did a good job respecting him and his needs in the moment.
Dogs don't have to be in actual pain to feel uncomfortable (though they may be). There are lots of things people do that can make dogs uncomfortable, and just because a dog initiates contact with someone doesn't mean they are automatically okay with everything that person does to them. Just because you were okay with hugging a friend, for instance, doesn't mean you'd be equally okay if the friend pressed his forehead against yours and held sixty seconds of sustained eye contact, or licked his finger and stuck it in your ear. Maybe she leaned over him, made prolonged eye contact, accidentally hit a sore spot, scratched in an unpleasant way, or was wearing the wrong perfume...no way to know via the internet, and it might have been subtle enough that you wouldn't have noticed it in the moment either.
Please don't treat this as an issue of testing boundaries. In terms of future unexpected growling, take him out of the situation (no need to make him lie down) and try to notice what triggered him so you can work on it during a better moment. Making a dog feel more comfortable about a variety of things can take several forms, but the most straightforward (and effective) is usually counter-conditioning. Other resources and thoughts in this thread:
http://www.dogforum.com/training-behavior-stickies/growling-86338/
You might also want to check out the threads on resource guarding and reactivity.