To me, it isn't so much a matter of custom built as much as hand built. When I build my wheels, I true the wheel then take the time to hand tension each spoke, then true the wheel a second time. This keeps the spokes from stretching while riding, losing tension and going out of true while risking wheel failure. Aside from a custom set being able to have YOUR specifications, that's the only thing I really like about handbuilt sets. You're absolutely right, most prebuilt sets can be trued at home or at the LBS, so that's not an issue. As for my personal experience, wheels that I build myself have always stayed true far longer than any factory built wheel. As for cost, it's about the same. I'm building a set of 24/28h wheels on record hubs for about $300.