So for all practical purposes the system is basically unchanged.
I was upgrading multiple legs and actually used the certs out of order, by mistake. The agents didn't check the flight segment info & the confirmation number on the cert didn't match my LH reservation either. (A UA mistake) I think as long as your name matches and the GPU is still valid you won't normally have issues.
I was pretty happy with the process and went 4 for 4 on my upgrades on this trip, 3 on LH, 1 on UA. It will be awesome when we can just do this electronically, especially if we can confirm the upgrade before arriving at the airport as LH seems to open up space at about T-24.