Hi @holybuble, I think the book assumes you have some background in Dramatica theory, where the distinction between MC and Protagonist are spelled out, so it doesn't try to explain that. I'd say it's not so much that the book misses the distinction, more that it spends very little time on the archetypes (of which Protagonist is one), teaching you how to build complex characters instead.
I too have enjoyed Dramatica for Screenwriters. If you have a story idea bubbling in your head, I'd recommend to go through and do the exercises as you're reading it, as I found them extremely valuable! (After all there's no time like
The Present -- sorry Dramatica joke)