Custom is sometimes the only way to go if you have odd body geometry or quirky riding positioning. Most people can go with a stock frame and just switch out crank length, seat post, stem and bars, and they're good to go. Heck, I'm 6'6" and I was able to go stock on my new bike, with just a swap out of the stem to adjust the reach properly according to my fitting.

The big benefit to custom is being able to get precisely what you want. Do you like to stretch out? You can get a longer top tube and not have to throw a big long stem on there. Wide tire/fender clearance on a compact geometry frame? Yeah, you can do that. It's all about how much you have to spend on the build. A stock bike will typically last you a long time, but a custom bike really is an investment in your cycling comfort.