I thought so too, but I was in CHC recently and the EK staffer processing it said, hey, there's an offer here - and it was the 20% discounted mileage cost for the upgrade.

However, I think it does need to be done using the EK ticketing platform, as I also recently did a check-in upgrade at a different station where the staffer (outsource) did it manually at the desk (i.e. airport control system) using published mileage rates and that hasn't had the discount applied (but in that case it's only a couple of thousand miles so I didn't want to make an issue of it).

So I think best not to do it at the check-in desk itself, but go a little earlier and do it with the EK staff member at the standby/control desk, or at the lounge, where you've got more time and better luck on them using the system which can show the automatic discount.

Or....it could be a bug and it shouldn't be allowed, EK IT and all