My TA mentioned that if she does that and the airline she tickets on doesn't agree with her pricing, her agency will be subject to a chargeback for the difference.

If the difference of opinion involves interpretation of a rule, the cost could involve a couple of point-to-point fares needed to bridge the controversy, and amount to a tidy sum. So except for very vanilla routes (beneath the interest of many FT'ers, I daresay) I'd be surprised to find many agents interested in taking that kind of risk for OWE's.