They're made to fit a typical person. That leaves most of us with a bike that doesn't quite fit. Getting a custom built frame solves this problem by fitting the bike to the person, not the person to the bike. And buying a stock bike means that you get whatever components that the manufacturer wants you to have, and that might not be your idea of a good bike. If want something different, that's built just for you, it's time to custom build.
Fit is always the most important factor when buying a bicycle.
But, it's not always easy to get a good fit. If you have a long torso, then you need a long top tube. Otherwise, you will end up sitting too high on the bike and you'll feel cramped. You could put on a longer handlebar stem. But if you use a really long stem, you'll be moving too much of your weight forward over the front wheel, which will adversely affect handling.