I'd agree with Chestnut, always insist on a proper walk around with the rep and proactively point out scratches etc too if you find any.
That said, I tend to find if you pay the small amount of damage waiver they tend to be a lot more generous (not that I've ever hit anything in a hire car but it reduces the pain).
I can see why some damage is not repaired, however the big question is why charge if it won't be repaired? Makes more sense to charge a fixed price for damage found but not repaired.
2015 500X Pop Star, 1.4