Typically I believe that a “stock” stem will better serve a customers needs than a fully custom stem. Stock options are generally less expensive and much lighter weight.
That said, I am currently working on bike that will really benefit from a handmade stem. The customer has ordered a stainless touring bike with handlebars that are level with the saddle height, this normally isn’t very challenging but he also wanted to stay will a more traditional looking level top tube. To avoid using a huge stack of unsightly spacers under the stem I have integrated that space into the steer tube clamp portion of the stem. Once painted, this custom stem will really help keep the bike looking clean and tailor-made for the rider.
As part of a new bike, or the restoration of a classic, the aesthetics are the primary reason behind custom stems now. Matching the geometry of the bike and/or adding small details like the custom bell mount shown are considerations to be taken into account.