Either the dealership, or CarMax, who ever gives you the best price.
The dealership has records on the vehicle so they should be able to price the vehicle a bit higher than CarMax, but they also have record of this issue with the bolt. So they will want to cut the price to cover the repairs they will have to make.
I would not take in price drop, because they have not diagnosed a issue. Dealers love to play this game about "maybe"
If you have already had the vehicle looked at for this issue, and 2x they have updated the computer. There doing the work they know they can get paid for. Computer updates take minutes to perform.
The dealers GFF is kind of like diagnostics for dummies the computer looks through all the codes then tells the tech what should be done next. This is not about fixing the vehicle this is a way to buy time.
First thing the computer wants to do after reading codes is update all modules in the car that it has updates for. This is all done in 30 minutes while the tech looks over the vehicle.
I'm guessing the tech heard engine noise and guessed that the oil pump bolt was the cause, and played on the computer for a hour and they called this a diagnostic.
First I would go back to the dealer and ask they diagnose the oil pump bolt issue one way or the other. Is it broken or not. You have taken it to them 2x for a check engine light, they should be able to say one way or the other if the bolt is broken, backing out, loose something other than a guess.
As for price, this issue in a lot of cases requires a new engine to fix the problem because when the bolt finally does break or back all the way out the timing components get destroyed.
I would not let this cause you to drop the price much, and I would also get second opinion. Google search your area for Audi/VW repair shops. Bound to be one somewhere close by. most of the time these are run by dealer techs that decided to open there own shop. they have all the dealership training and in most cases the same scan tool and the same ability to perform the same repairs.
I would not tell them what the dealer said, just have them do a diagnostic and see what they come up with.
For price maybe, consider knocking $3000 off what ever trade in value is.
A lot of the time the dealer will see a vehicle that has a issue like this, and the service department will come up with a bunch of repairs to scare the customer. The repairs are minor but as a total the price is to much for someone to repair all at one time. So the customer sells the vehicle back to the dealer. The dealer gets a great pre owned vehicle they can sell again after little repair. and the dealership gets to sell another car.