The idea of a custom bike is a valid idea, but I have followed a number of custom bike stories from idea through construction and in a significant number of cases the resulting bike isn't exactly what the buyer had in mind. Sometimes the difference caused problems and sometimes it was not a problem, but a difference of expectations between the builder and the customer. In any case one nice thing about production bikes is you can validate how you feel about a specific model based on reviews, owners reports, test rides, etc.. and when you get the bike you can expect the product to be the same as the bikes you researched.
I bought an expensive touring frame recently - the cost was at the lower end of the custom frame spectrum. I considered a custom bike, but realized that since my body is normally proportioned that I preferred to have a nice production frame I could count on than a custom frame that might suit me a bit better, but also might disappoint me. In the end I've been happy with my choice.
Very good points. (I think Seven can be considered semi-custom.)
If you don't have any particular issues you are trying to address, an off-the-peg bike is the much better value. At the least, if you crash it, it will be much cheaper to replace!