Why don't frame manufacturers ream/face their frames? Before building up a new frame, it's crucially important to ream/face the headtube and crown race seat (and the bottom bracket, if using press-fit cups). You should also ideally chase the threads of the BB and the derailleur hanger.

But why don't manufacturers (e.g., Surly) do this before they leave the factory? Surly in particular mentions that they do in fact face their head tubes, but they do so before painting the frame, requiring new frame owners to re-face them.

Why wouldn't they just do this before shipping the frame out? It seems like a no-brainer.
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.