I just built up a bike on Soma's Fog Cutter frame. My usage will be road sport riding, gravel and dirt paths, and randonneuring up to 1200km. If I were going with a custom frame, aside from a custom fit for my 6'2" long torso'd body with an inflexible lower back, to the Fog Cutter I'd add:

third water bottle braze-ons, front and rear internal dyno wire routing, light brackets, pump peg, chain hanger, and front fork mid-blade mounts. Aesthetically I'd prefer a dead level top tube. While we're add it, maybe turn those mid-blade mounts into water bottle mounts for uber log dry days.

For things like types of BB, headset, rear spacing, and axle type, I'd talk that over with the builder. The rear end of the Fog Cutter, with QR 135mm disc, is becoming uncommon.

I'd have two sets of wheels - one for pure pavement and one for gravel and dirt paths. I'm not a huge 650b fan, but maybe for the extra tire width I'd have 700c and 650b wheelsets.