A related question that's been in the back of my mind for a while - does the waiving of an upfare charge apply to tix purchased through a TA/OTA?

I have to book all of my corporate travel via an OTA and have been occasionally tempted to upfare some domestic longhaul. But I wasn't sure if I could call AC and do that in this case. AC seems to tix not booked through them as lesser citizens to some extent.