Perhaps not. Often their 'quality program' repairs are based on an unacceptable number of whatever from a particular batch going bad. a BTO system might not have used that batch. They would know the serials that used those parts.
Also from reading his blog it sounds like he went in screaming that they needed to give him a whole new machine because his GPU which might have been fine, was the same kind as one that a batch had an issue. That's not how the game works. You don't get a brand new machine because one part is perhaps bad.
Also, when he took the machine in with an issue it wasn't the GPU but the logic board, which didn't have a quality program and his Apple Care was expired. But he decided to yell and scream that no they are idiots and lying that it was the logic board, he is an expert and he knows that the whole thing was from the GPU they didn't replace when he told them to give him a new machine some 2 years before. etc.
If the tone of his blog, which reads like he acted like a screaming asshat, is even close to the truth then I can see why Apple Care, Customer relations etc kept saying no to him. He was asking for things that are not part of the terms of the system. Truth is that this judge was possibly in the wrong because he didn't have all the facts regarding why the program existed etc but since it was just small claims court which maxes out at like $10k if that much, Apple wasn't likely to really care that much. If someone tries to use this case as precedent they can still bring out the big guns of the full facts.