But, why not have the full line bike shop just offer a more sophisticated setup for riders who want them? Seems like I have seen this before where 'regular' setups are included with a bike and the high tech ones aren't free.

I also used to shop sometimes at a boutique shop like you are describing, but I didn't really like it because they had very limited selections. I only went there because it was very close to my house and I usually only bought gels and stuff like that. The one time I had my bike serviced there, they tried to sell me a whole new groupset, and when I objected, they just replaced the ferrel on my RD cable and it was magically OK. Not saying all boutique shops would operate that way, but this store had lots of high end customers who bought very expensive bikes on a whim, so the temptation to make a fast buck was alway there. I actually saw it go down once with some business woman buying a very sweet bike on her lunch hour - she was obviously more interested in the colors and how everything looked than anything else.