I was told pretty much the same as K1W1.
I was given two keys when I bought the bike, one had a red sleeve over the business end.
I was told to guard this 'red key' with my life; it was the master and without it replacement keys would cost me a small fortune. I obviously know my PIN but that wasn't mentioned with reference to the keys. Not saying the dealer was right but that's what I was told.
Your dealer was (are you ready for this? It shouldn't be a surprise by now with wherever you bought it given all of the other stuff you've posted) totally wrong about that.
The red sleeve over the spare key is just a protector sleeve. There is nothing magical about that key and they are both completely the same.
All of this "master key, spare key, red key, black key" (say it with me, Dr. Seuss) misunderstanding junk is a holdover from the days when Ducatis shipped with three keys - two black keys, and a magical "red key." The red one was the master key and you needed it if you
ever wanted to be able to reprogram a new black key to work with the bike's immobilizer. It was a stupid system because if you ever misplaced the single red key you were screwed, so Ducati stopped using it. The process was introduced with the 999 / 749 (I think) and while I'm not entirely sure when exactly they discontinued it I think it was somewhere in the 2010-ish timeframe.
Anyways, the important thing is that
there is no more "red key" master key system with Ducatis. Both keys you get now are the same, and they'll both work to program new keys. As long as you have one, you're fine.