Bob was tapping into some wisdom when he said to trust the manufacturer to have faced it square with the thread bore. That said, you do want full thread engagement for best performance. I personally have done what you proposed earlier, to flip the plate and machine the boss. Flipping the plate does not change the axial relationship of the threads between spindle and plate, that relationship is already set by the manufacturer for you. On my lathe, I need to take a little out of the ID on the boss that protrudes from the back of the plate to fit the step behind the threads on the spindle, and then shorten the boss until the midpoint of the threaded portion of the hole aligns with the midpoint of the threaded portion of the spindle. You will have a square shoulder to butt against and more secure thread engagement of the chuck plate to the spindle for doing so. Just be sure you don't cut it so short that the bolts on the plate (or anything else) interfere with your headstock, so measure thrice and cut once.