I booked through the agent because they can see some fares I can't get from .bomb. For example, for a OW ticket, the lowest I got from .bomb is M, while the agent booked me into L/S, which is about half price of that on .bomb. In other cases, I booked B fare in order to use the sales upgrade cert from the agent.

Also, I don't see any difference for UA between booking through an agent (but charged directly by UA) and using .bomb.