Interesting discussion in this thread, if you have the time to read it all. A lot simply boils down to how much money someone is willing to spend on a bike, and the perceived value in their choices. To add my personal experiences, I have three touring bikes -- one of them production (Soma Saga), one of them small-scale production (Bob Jackson World Tour) and one fully custom (Waterford RST-22). All three of my bikes have similar quality components, generally Ultegra-level Shimano.
I bought the Bob Jackson frame and fork new direct from England, but it is "off the peg" and not custom. I got it for commuting and have ridden a few loaded tours on it. The frame has a lot of old-school class and charm, but the frame construction and paint is a little sloppy in spots -- although certainly not bad considering its cost ($600). It is a great frame for commuting and light touring, but I have found it wobbly and not stiff enough for loaded touring unless the weight is carefully distributed between the front and back. It also does not have clearance for tires larger than 32 mm with fenders.
After several loaded tours on the BJ, I bought a Soma Saga frame and fork for my dedicated touring bike. The quality of construction and finish are outstanding, particularly for a frame and fork that cost only $500 new. The frame is designed and constructed much better for loaded touring than BJ, with larger diameter tubing, longer chain stays, a taller head tube and more clearance for larger tires and fenders. It is rock solid when loaded with panniers, and distributing the weight front to rear is not so critical for handling. For the money, the Saga is an incredible value and all that I need in a touring frame. The geometry fits me perfectly.
My Waterford is a fully custom frame, but I bought it used. Fortunately, it fits me perfectly and I wouldn't change hardly a spec if ordering one new. This is simply the best bike I have ever owned. The quality of construction and finish are outstanding, although it could use a new paint job after 10 years and thousands of miles riding. The Waterford handles and rides better than any bike I have owned. It has clearance for larger tires and fenders, mounts for fenders and racks, and canti brakes. It was not designed for heavy loaded touring, yielding a much more compliant ride than my full touring bikes, but it could easily handle rear panniers with a fairly light load (eg, 20-25 lbs). As much as I love this bike, I could not afford to buy one new. A new Waterford identical to mine would cost more than $3,500, which is much more than I could justify spending on a frame and fork. However, I bought it used for only $600, so it was an incredible value that I was lucky to stumble across. I am considering having it repainted by Waterford at some point, and it would cost me more to have it refinished than I paid for it!
Bottom line: You can buy an excellent touring bike for a reasonable amount of money that will more than satisfy any ones needs. However, if you have the money to spend on a custom frame, you can certainly improve upon the appearance, quality of construction and fit of a production bike. If you find a used custom bike that fits you for a reasonable price, jump on it!