I too was under the impression op-up's only happened after check-in closed.
I've had maybe 2 or 3 op-up's with BA and IB, all done at the gate upon boarding. One time on IB the agent rather dramatically ripped up my boarding pass without saying anything, so for a few seconds I thought I was being offloaded and denied boarding until she finally said I'd been upgraded and handed me a new boarding pass!
With Qantas upgrades would occasionally happen in the lounge, names would be called over the PA to come see staff at the service desk.