**First** thing that comes to my mind is labour costs.
**Second** thing that comes to mind is that once you break that paint seal by reaming/facing you are allowing contact with the air and elements. As a good practice you should coat the threads with a little grease before assembly, meaning that when you get that new frame, you tap out the mounting holes and then screw in the mounting bolt with grease that will re-seal the exposed metal.
**Third**..tradition. New frames never came faced in the old days as it was expected that the professional bike mechanic would be doing all that as it was their job.