I would be concerned about 'unearned fees' in this case. It would never occur to me to keep any portion of a 3rd party charge over and above the charge.
If my FI were to charge a review charge, for instance, it would belong in 801, so I see no correct thing but to refund this difference. It really has nothing to do with tolerance...it has to do with overcharging and keeping an unearned fee.
In addition, what you have actually done is padded your tolerance as the higher amount shows on the GFE side and a lower amount shows on the HUD side...tolerance is allowed for the opposite (actual cost higher than estimate).http://www.bankersonline.com/regs/12-1024/12-1024-014.html