Your builder should be able to give you a good recommendation since you've got the two bikes to consider. I assume that as a custom fork it will have a steel steerer tube? Carbon steerer always have a max spacer height. Not sure about steel. You can always start threadless and go threaded but not the other way since the steerer tube gets cut.

Threadless is lighter. Probably easier to find a greater variety of stems in different lengths and rises, and therefore play more with the fit of your bike. Threadless allows you to change stems without pulling the entire front end apart. I don't think the brake hanger cares which way you go. The shim looks just like a narrow silver spacers and belnds in with a silver Nitto stem.

You can always start threadless and go threaded but not the other way since the steerer tube gets cut.