Well, I am of the belief that the factory spent considerable time and money engineering something to work a certain way. If it left the factory without something on one (or more) alternator terminals, then it likely didn't need it. I drive a Volvo with an ISX Cummins engine and the alternator on it has a couple "empty" terminals as well.
Now, as to the low voltage for the first couple miles, that's another issue. Could be voltage regulator beginning to fail - or just dirty/corroded connections. Belt isn't slipping, is it? You try giving the engine a few revs to see if the alternator "kicks in" after start-up?
*Edit* I re-read your post and see you've revved the engine to see if it charges. Check to see if the alternator is turning at full speed/belt not slipping. Loosen the belt and turn alternator by hand (Engine off, of course); see if it turns freely.