That's a tough one. I think I'd go off the rack. Bikes retain their value well, so you can always sell it and go custom later if you have issues. But, if you want something unique, custom might be better right from the start. All of my bikes were custom builds, except my first, which gave me an idea of how I like be set up.
Another reason to go off the rack is because it is your favorite lbs. That would be a big part of my decision.
'02 Eddy Merckx Fuga, Selle An Atomica
'85 Eddy Merckx Professional, Selle An Atomica
'10 Soma Double Cross DC, Selle An Atomica
Slacker on wheels.