Even people building up bikes from a frame/fork are not getting a custom bike. They are using off the shelf parts to build their ride. I built up my LHT from parts...their isn't an identical Trucker on the planet, but the only part on the bike that is actually custom is the mud flap I made from a milk jug.
Mixing and matching production parts is a cost effective way to get a specific set of performance and aesthetic results with minimal risk. I can use some Shimano Dura Ace barcons with SRAM Jag Wire cables and a XT reverse rise rear derailleur to get my LHT to shift with little risk, reasonable cost and it meets my preferences, but it's not really custom. Not one of those parts was made for me to my specs. The bike industry is just standardized enough we can mix and match a fair bit.
If the parts we use on our bikes weren't made in the thousands to a common standard of functionality they would just be way too expensive to use and wouldn't be particularly versatile. Although we treat custom with an implied assumption that it will be better than production I don't think that's necessarily the case. Production parts & frames have lots of things going for them.
If you have me the option of a production Riv and a custom bike of equal value I'd likely choose the Riv because I'd know exactly what I was getting. Both in terms of function and aesthetics.
There are really three kinds of bicycles, at least for this purpose, production bikes, semi-custom and full custom (sort of).
Production bikes like the Surlys, Rivendells, Treks, etc, have a good mix of components for the average rider in that class of bicycle, although you do have to put up with whatever the factory puts on it component wise, or expect to change things out. Your also stuck with whatever the factory decides is a good paint colour that year, and sometimes what they choose make you wonder if they been smokin' some really bad stuff lately.....
Semi-custom bikes start out with a production frame, but allows the buyer to pick and choose components, they want, good if they want something unusual, like a touring bike with a disc brake on the front and drum on the rear.... Almost needed these days for a rider who wants more then one spoke on a racing bike wheel....
Full custom allows the buyer to have a frame built specially to their needs, this is good for someone who is an unusual height or build. For example a guy who has the height to play pro basketball, may have a hard time fitting a production frame, a person who could easily fit in with a group of munchkins, would have a difficulty with a production frame, a person with an unusual build, like short legs and long torso or very long legs and a short torso, can benefit from a custom frame. Heck a guy who is normal height but wears size 14 shoes can benefit from a custom frame that has the right build to reduce toe slap and heel strike.