First of all, nobody is CNC machining airplanes from billet. They're sheet metal structures. But that aside...
For handmade structures with little tooling, the difference is less because it takes only a bit more training and about the same amount of time to make a bunch of unique parts as to make a bunch of identical parts. The economies of scale are there, but less so.
But even for CNC parts, extra shapes means extra CNC programming time (expensive but amortizes over the number of pieces made, so n unique parts costs n times as much to setup and amortizes n times less). It means more inspection gauges. More tooling. Significantly more inventory costs.
Design a machine from a single modular piece, and all else equal it will be much cheaper than one made from a bunch of unique parts.
When you machine an amorphous or crystalline material like a metal alloy you aren't always simply removing material, but can be putting a specific finish on the surface for mechanical reasons. Sometimes you want to cast again for performance (or cost) reasons because machining can't get you what you want.
When you build a shape from a composite material such as fibreglass in epoxy you want the longitudinal fibres to run long distances to distribute the stresses. Machining it would defeat the purpose. They are cast.
I like these blended wing designs; I'm just pointing out that your argument is not applicable to this application.
Airliner structures are very conservative. They still use a lot of fasteners, lowering manufacturing and structural efficiency.
There is a lot of room to improve. There is a huge space for innovation in composites. It just takes a lot of time and money to ensure the more modern methods are also durable and safe.
Imagine how efficient car maintenance would be of only we'd use one standardized car. You can have the larger model, but all components are the same, every garage has them...