It's a cluster all round and from here then I can't see any happy outcome really. You're going to carry on a nagging thought everytime anything creaks / squeaks on that bike and every dealing with the LBS is likely to leave you suspicious.


Anyway, now you've dinged it, then I would say that you need to go in with a couple of coffees, sit down with the LBS owner and see what way you can both come out of this respecting each other and balanced. To me would be unfair to leave the scratched bike / mech with the LBS, equally he should have come clean with you about how he was giving you the frame / build you wanted. But don't go in there all guns blazing, that's not going to work for you, as I say, do the whole olive branch thing and that is the surest way to get a positive outcome.

Which is a shame, as to be fair a 'custom' build like that is actually potentially a positive, as I would rate the mechanic in the shop where you are going to be physically present to be a fraction more careful than the factory. FWIW then I had something similar happen many years ago, but for a different reason. Specialized EPIC MTB I was after was sold out worldwide. The shop could get the model down, and happened to have the entire groupset someone had taken off an S-works to swap to Shimano. So the frame was the same, but a different colour. Anyway I got what I wanted for a good discount, and 2 months later when the frame cracked I even got the colour I originally should have when they swapped it....
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Be reasonable and think outcomes here. What is it you initially wanted, DI2, ok, was a 1 button shifter essential or what you desired, or is it just because you thought you were getting the 1 button that you mentioned it? If it's an issue then can they be swapped? Be clear what you think needs to be done to make you 'happy' and equally be reasonable if something is just 'different' but not material to your bike's performance or your enjoyment of it.