I’d say this is clearly a case of happy, contented tooth-grinding aka tooth-purring. Esp young bunnies can do it in many situations, not just when they are being pet. Some can do it in their sleep even.
A bunny that grinds is teeth from pain looks very uncomfortable, sits bunched up and is not eating happily etc. A painful tooth-grinding is choppy, more of a chatter. It’s not easily confused with anything but discomfort and esp since you are familiar with animals, I’m sure you will know it if you’ll ever have to experience it.
Bunnies are as a rule not over-joyed at being picked up. baby bunnies tolerate it better than adults, some babies even seem to enjoy it. But since rabbits are like the prey species of prey species, they have deep instincts telling them that being picked up is very risky. Most bunnies love to cuddle and be pet, but on their own terms. It sounds like your bun enjoys being pet a lot, at the same time as her instincts tell her to be a bit wary. She is also about to start puberty.
To me she sounds like a very happy, healthy normal bunny. I bet she’s very pretty too =)
ETA: I don’t think bunnies tooth-purr out of annoyance. But they absolutely can become very annoyed if you stop petting them sooner than they think is appropriate.