Actually there is a third category, semi-custom.
Custom allows you to design exactly what you want and the assumption is that no production boat is that. Now it can also be a
builder that is only custom. You'll see more custom in
aluminum and
steel as there's no
mold involved and not a huge cost difference. In
fiberglass, a custom costs considerably more than production because no boats to spread the costs of the
mold and tooling. Custom might do something that production boats don't, but, depending on the
builder, could have issues too.
Semi Custom typically has a production
hull so the cost benefit of that but allows you to customize the
interior to meet your own desires. Some allow everything to be customized and some very little.
Production has advantages in proven design, cost, and time to build. However, your ideal boat may not exist as a production boat.