That doesn't square with the facts. If there were warped rotors and if the brakes were not capable of stopping the vehicle effectively you would think those symptoms would have been the first words from the OP, but he has been silent on both counts. That suggests there is no pulsing or diminished braking capacity. SDomeone suggested he try pumping the brakes while the vehicle is sitting stationary and the OP responded that didn't help.
Nobody has said anything about magically getting fixed. He said the Mechanic told him he was the one that did the fixing.
There is no good theory that fits the facts presented. The only thing known for sure is that certain facts have been carefully omitted. It's anyone's guess what they might be. For all you know the brakes may now work 10 times better than they did before the work was done. You and the OP don't seem to care how effectively the brakes stop the vehicle. Your only concern is how far the brake pedal moves - that's ignorance.
If only part of the Master cylinder bore is scored or pitted that will be exactly what happens. It is not that unusual for a master cylinder to leak for only some part of the stroke. Just because you fail to understand how something works doesn't make it magical.
-jim