I would put steerer and headtube dimensions fairly far down the list of what's important in a custom frame. For me, #1 - the builder, the bikes he favors building, and are we on the same page? #2 (closely related to #1) - the bike fit. #3 - do the details he prefers to build with work for me? I put head tube /steerer in this category. A lot of excellent bikes have been built around all the standards. (Look at all the great bikes built around 1" standard steerers and steel forks over the past century.)
Different builders vary a lot in how comfortable they are working outside their "normal" practices. Some will say "I do it this way. Go to someone else if you want different." Others view the same request as a challenge they love taking on.