Depends on how the roof rack is held on. If you have silicone between joints, then you'll have to clean it off and reapply, etc. But if it's plain nuts and bolts, I'd remove it to get to normally neglected areas.
It would not be considered overboard....it would be considered Autopian
I just polish and wax with my roof rack on. I'm not sure about your roof rack, but mine has adjustable crossbars that I just move all to one side when doing the roof. It gives me more room. If not, just work around it, it shouldn't be too difficult. I polish and wax my roof rack with it on the car too.