On the passenger manifest, there is definitely a remark for those passengers that have been operationally upgraded. On a number of occasions, the MC even came talk to me and specifically mentioned it (in a pleasant way, such as "so happy that we could offer you a better seat up here").

Lest I remember, being on an op-up never had any impact on meal priority, they still treat me based on elite status order. However, when on an op-up I usually tell them that I'd just take whatever they have left after the paying pax. Which usually means that I get exactly what I want, plus unlimited chocolates afterwards.

In the OPs case, the FA was probably just a bit clumsy in that he started asking the OP for his meal, and then noticed on the manifest that the OP was on a courtesy upgrade. I agree that at this point, the FA should have just taken the order anyway. But really, that seems a very minor point and no basis at all for a complaint.