I had a custom build (well no custom wheels) and I got a broken down quote, so you should just "harmlessly" ask for that and then point out "but ooh, I think the bars go for like xxx dollars".... - sure you're entitled to a breakdown for the kind of $$ you're spending. And you're entitled to some back-and-forth about parts too.

the 100 build premium, well, maybe you pay for the future support and all.
I didn't pay any surcharge, but then again it was the guy's own frameset so maybe the 100 were included its price already.

I also got about 10% off the total, and he threw in a pair of bibs and a jacket. Expo discount, he called that.