There are a few manufacturers that make custom Carbon Fiber frames too. Parlee, for example does full custom carbon builds.

"Carbon" shows up quite a bit on this list.
Directory Of Custom American Handmade Road Bike Frame Builders |

Other common custom building materials include Titanium. Also, a few very high end steel & stainless alloys. And some of them are unbelievably lightweight.

However, I'm not sure I'd call setting the seat in the right spot, and getting the proper stem a kluge. Usually setup is part of a LBS selling a high-end bike (they may not do a full configuration for a demo ride). Uncut steer tubes are often quite long for maximum configuration flexibility. Your demo bike probably didn't have a full uncut stem.

A super-high bar position may be a flexibility issue... and may be something that would change with more time on the bike. You might compensate for a high bar somewhat by using a shorter stem. Nonetheless, using a tall steertube/stem, you may choose to lower it after a few thousand miles. If you use a tall headtube, you may not have that option (easily).

And, really, there is nothing wrong with using a tall steer tube or stem (up to a point). Keep in mind that a road bike isn't an upright bike.