Problem #1. The Aux coolant pump was probably the issue from day 1.
Problem #2. The mechanic probably didn't know that there was a aux coolant pump under the intake manifold.
Since this is a 2003, I highly advise changing the original pump out with the revised aux pump that bolts to the front of the motor instead of under the intake manifold.
As for the labor, replacing the aux pump typically requires removing the intake manifold to get proper access. Some people say that it can be done without doing so. Personally, I just can't see how one gets their hands into a 4" high opening and manuever a ratchet or hose clamp pliers. There just isn't a way to do it.
As for the replacement of the timing belt, sepentine belt and main water pump, I'm guessing that your son hadn't had it replaced at the 75K mile replacement interval and thus the mechanic believed that the main water pump was faulty. The funny part about the aux pump is that when it leaks, it is a very small leak at first and most of the leak pools in the top of the engine block and evaporates from the engine's heat. You smell a leak, see a lower coolant level in the reservior but, you find no evidence of dripping or the source of the leak. This is always a aux pump failure.
Sadly, the mechanic who did the job must have believed that there was only one place that coolant could leak from on the 2.7T.....
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