Different draws from the same question bank or different question banks?

Hello! I recently completed a very similar training course where there were 3 groups of individuals that would have to answer some similar questions but some questions would be different based on their job role. I completed this by following your option 1 and created one question bank to pull from which ended up saving me time in the end when the wording of the questions had to change. I also had to delete a question from all scenes which was easier to delete from the question bank instead of each scene separately.

A few tips that I found helped:
1) If you have not already created all of the scenes, finish one and have it approved (if that is part of your process). Once approved, duplicate the scenes to save time. 
2) I made a list (outside of Storyline) of which question numbers go to which scene. This helped prevent the risk you mentioned about not marking a question correctly to Always/Never. I found it easier to track outside of Storyline (Excel/Word, Google Docs, etc.) a simple list of each scene and which question numbers should be "Always" or "Randomly". 

I included an image of one of the Draw Questions from Bank window to show how I set my up. I hope this helps!