Even high-end over the counter rifles are made to suit a wide selection of people, so despite spending what might seem to be a great deal of money, the end product might not suit you as well as a custom. The custom rifle doesn't necessarily do anything better, but with it, you can do better, provided that the custom features you select have to do with shooting and not just aesthetics. The man who understands what it takes to shoot well under the conditions he wants to use that rifle in will benefit from the custom rifle, but the novice might not.
The best advise I can give someone who is a knowledgeable shooter but new to the world of custom builds, is to look at your current rifle and determine what it is about it that you would change, and then try to imagine how a custom rifle might improve upon that. It might very well be that an over the counter rifle will work just fine with a bit of tweaking to address its short falls, say for example you don't like the position of the sling swivel or the fact that you new rifle doesn't have irons.
I've been thinking for sometime about having a switch barrel made. Provided I keep to the same barrel contour throughout my cartridge selections, I need only change barrels and perhaps bolt bodies, while keeping the same stock and scope, which over the long run is significantly less expensive that purchasing or building complete rifles for each cartridge.