Can a branched course (two tracks) result in the user completing one scored assessment OR the other?

Yes. I have created quizzes with 1 path of questions for the majority of it, but then 2 paths based on if the learner is or is not taking one section of the larger course (which also branches based on the selected path). At the end of the quiz, the 2 paths converge back to a single Results page. On the Results page's Quiz Settings dialog, I have ALL of the quiz questions selected; at the bottom of the Quiz Settings window, the Only score viewed questions checkbox checked.