I've built up my last three bikes- cyclocross, road touring, and bikepacking, all from Soma frames. Here's some of what I've gained:
The perfect fit for me. I no longer need to convince a shop to swap out stems and cranksets to accommodate my long legs and shorter-than-average torso.
Gearing suited to my aging legs and my continued desire to cycle tough routes in remote areas.
A deeper understanding of frame geometries and the way components operate, and work together.
A bike built with durability in mind.
An embarrassing collection of bike tools.
An intimate knowledge of every bit of my bike.
The reassuring confidence that I can maintain and, if necessary, repair the bike when on tour.
The sheer fun of selecting all the bits and pieces, then putting together a functional piece of art.
For me, all that is well worth extra dollars and hours.
And, on the original question- I find down tube shifters easy to use, simple to maintain, and very long lasting. My 1985 Trek touring bike, which I just retired from loaded touring duties a couple years ago, has the original shifters, which still work flawlessly. I put them on my cross bike a few years ago and love the look and functionality.
On my current touring bike I have 9 speed dura ace bar ends, indexed with a friction option. They are also a pleasure to use.
Of course, I love the elegance of a quill stem, too...