Recent DP: I upgraded a colleague both ways from YYZ-VIE. I requested the first leg at the concierge office at YVR. They were unable to process the upgrade for some reason, but were able to call someone at YYZ to do it. On the return, the check in agents at VIE couldn't process e-upgrades at all, claiming they can only do cash upgrades. I called the concierge line and they were able to sort it out. I wasn't asked to pay the add on fee in either case. They upgrade was PY to J.
The fee was waived either because I am SE, and therefore my rules applied, or as a favour due to glitch. I'm not sure which.