It depends on how custom is custom. If it's really custom-made, it will take into account some factors that a production frame can't. For example, if a person is either taller or shorter than average, it can make a big difference, because you start getting into more extreme differences in the proportions of leg length versus torso lenght, length of arms, proportion of femur versus tibia. There's no way a production bike can take these things into account. The tubing choices will also be more in keeping with your weight and intended use for the bike than what you get in a production frame (which has to account for everybody rather than just you).

But pricey!? Have you looked at the prices for some of the higher-end carbon bikes lately? Geez, you can get two and maybe three custom made fine steel frames for the price of one of those. I'm reminded of the guys who go out and buy an $8000 carbon bike to commute to work on so they can save a few bucks on gas.

In addition to everything else, a quality custom frame from a good builder may have handling characteristics that no production frame can match, qualities that would appeal more to an experienced road riding enthusiast. For example, production bikes have to neuter their handling a bit so that buyers of all skill levels can ride safely, whereas someone who buys a custom-made frame might might want the kind of bike that offers high-speed stability more than low-speed stability.

But in the end, it's just very nice to know that the bike you ride is truly an extension of your body. The only problem is that a custom may require a long wait. I remember waiting the better part of a year for mine. That can feel like a long time.