"Put the value of those benefits on top of base pay, and use that gross as the salary when making the total income calculations..."
Er, no. The point is we *want* people to have good pensions and to have paid sick leave and to contribute into national insurance. That's kind of the underlying point of this. Contractors pay way, way less tax than anyone else doing equivalent work. They aren't spending the difference on sickness insurance or extra pension contributions or voluntary NICs, now, are they?
(FYI, next time you're on site, ask some of the civil servants how their final salary pension is doing. I'd recommend having a swift exit route planned.)