Mileage upgrades always have priority over op-ups, except for op-ups that have already been handed out. I sometimes received op-ups at check-in, which I assume the flights were so overbooked and the higher cabins were empty enough that CX did not need to wait for instant upgrade requests to start op-ups.I was once asked whether I would like to do an upgrade at SFO check-in (that was the only time I was ever asked). I declined and did not get an upgrade. Someone else probably got an instant upgrade.
I was asked once as well in TPE going to KUL via HKG. I was traveling with a friend who got my bulkhead seat after i got op-uped... thanks to the very nice check-in agent.