The primary reason I don't do it through the corp TA is that I get dinged with another service charge for them to process the upgrade, in addition to the service charge assessed when originally booking the ticket. Not only this, but outside of office hours, an emergency change phone number is to be used which has resulted in them telling me that putting through an upgrade is not an "emergency". I beg to differ.
Since they don't send an invoice for the service charge levied on the upgrade, I'm left with either eating the charge, or fighting with finance to accept my credit card statement as the official receipt, which they are loath to do.
Calling AC is just so much easier.