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Am I just complety confused?
Yes. If the face isn't square to the threads, there's more than enough clearance in a normal thread fit for the face to pull the thread askew, especially in the case of a BB cup where the face contact diameter is about twice the thread depth. Not only does that set your bearings out of parallel, but your thread flank pressure will vary wildly around the circumference, leading to either sheared threads or loosening in service.
I don't get the whole need to face the BB shell for external BB. Isn't the alignment of the BB dependant on the shell threading, not the face of the BB?
Am I just complety confused?