I know it's easier and cheaper to work with steel, but is it THAT MUCH easier and cheaper?
When you consider the overall outcome - the final bike, not just the frame, hand building in aluminum rarely makes sense. Modern aluminum factory frames are hydro formed into all sorts of engineered shapes that save weight and provide stiffness and compliance where needed. There is no way to hand build an aluminum frame even close to the characteristics of a mass produced frame. Perhaps when we can 3D print aluminum things will change.
If the custom frame customer is a "money is no object" kind of buyer, you custom build a carbon frame.
This leaves the customer having a budget to work to for the final bike. The weight savings of aluminum over a quality steel frame is about 500gram (much less with a custom hand build). However, the weight savings in putting the money saved working with steel into components makes a lighter bike with better components.
Frame builders will usually switch to titanium if steel is too heavy and the budget allows for more money to be spent. Its not as light as aluminum, but easier to work with.
If you look at the needs of customers that want custom frames, and are prepared to pay for them, you find they understand more about bikes than most of us, and therefore know how small a part weight in the frame really makes to the cycling experience, and will sacrifice a few grams for improvements elsewhere.
Mattnz's answer is canonical and addresses aluminum, steel, and titanium frames. Until we can easily 3d print metal frames, custom frames are going to be tube based. Hydroforming metal for one-off bikes isn't worth it and you can't easily braze aluminum (you have to TIG weld it).
But this leaves out another important material (as Chris H notes): carbon fiber.
If you want your own custom bike that has a radical (non-tubular) shape, you should do your own carbon fiber layups. This is something that you can do DIY as well as ask a custom CF builder to do.
And it can be literally any shape you want, within engineering limitations.