We had this very problem in the Ginetta G20s.. The rollcage was a little too low/level.. but this has been solved by welding on a 'bump' which raises the top of the cage by about 2.5 - 3 inches. Not too pretty, but a good move, plus not very expensive. Obviously the smaller drivers don't need this, but those of around 5'11" and above need them..
For the point of scrutineering, I can't agree with including this in scrutineering.. The car is checked for general safety and overalls and helmet. I would suggest that it stays as it is, but that when drivers are called to the assembly area that this is where it's checked - too late I know to make a change, but it's your safety that's being considered here, but I think it would be tough to object at that point from being excluded as you should already have checked this detail beforehand. Plus you'd only ever fall foul of this once...
EPS