I've had only small problems mailing in the Ent coupons. They want the coupon postmarked no later than the day after you make the res.
The itinerary doesn't actually get ticketed until sometime after the coupon arrives in Dearborn. That means that you can use a confirmed upgrade until everything settles down.
The only problem I've had is that sometimes the credit card info that they take over the phone doesn't stick with the reservation and they end up calling again from Dearborn to get a credit card number.
Because of the erratic charging of fees, I think it would be in your best interest to mention, so ever kindly, to the telephone res agent, that it is not possible to use the coupons on line, so you were hoping that they would kindly waive the fee as they are able to do. I could be wrong, but I have the impression that agents can manually override that fee.