I think this is a case by case basis, as it depends on many factors. You have to consider how the two QBs are different and similar to each other. How much will the play calling change when you switch the guys? How will the guys in the huddle respond to the switch? How much will practice time be spent on a specific playbook for a specific QB, if at all?
With that said, I don't think Golson and Zaire are too different from each other, that you have to dramatically change the offense and spend too much practice time tailoring a playbook to both QBs. Obviously, the popular opinion is that Golson is a better passer and Zaire is a better runner. However, both QBs are capable of running the same playbook in my opinion. With that said, if Kelly believes and wants to run a 2 QB system, similar to how he did against LSU(Zaire doing mostly running plays and Golson doing mostly passing plays), then I'm all for it. I don't think it would cause dysfunction internally on the team and I think this system could cause defense nightmares, as there a lot of ways to offset the defense with these two guys. I think the guys in the huddle would follow both Golson and Zaire leading them. Golson really hasn't been identified as a clear cut leader such as Brady Quinn, so I don't think the switch would cause internal confusion or favoritism. Zaire is an up and coming star and getting him a wealth of playing time now would benefit ND now and in the future, in my opinion. I will admit however, I'm on the MZ bandwagon and want MZ to have the offense to himself, but there's a reason why I'm not the head coach at ND.
GO IRISH!