It is only a guide and not a very accurate one. I have found all kinds of problems with these things when you start splitting hairs considering options. NADA obviously felt a need to increase pricing for the 318 engine over a slant six, they forgot to build in an over ride once you had told them to price a 340 based car. That should have prevented your ability to select an engine option for your 340 equipped base and the addition of their assigned percentage for a 318 optional engine.
You should write them and they will get right on that fix. It really would not be hard. It is tough to include all things into software when you are writing it. There will always be things missed, left out or simply do not work.