primi said:
Attached picture shows how I would like it to look. But that's not going to happen is it?
Not from Warmoth. It's not that they can't (obviously they can, because they used to), it's that it would look strange with the current fabrication techniques. They've gone to a "double lam" top, which means the top is actually two pieces thick: A solid top that's carved, and a laminate over that to present the exotic woods such as quilted/curly/spalted/burl Maple, Zebra, Koa, Pau Ferro, etc.
DL Tops follow body contours, with binding on the edge
So, if you recess the knob/switch holes, you'd see the separation between the thin top laminate wood and the underlying carved top, whatever wood that would be.
It's a cost/waste issue - attractive exotic woods are getting expensive to the point where even the expensive American labor involved in laminating a top is cheaper than cutting off a thick chunk of something exotic that you're going to turn most of into sawdust.
However, depending on what species of wood you're interested in, it's possible they could to what you want as an offline operation. It wouldn't be in the builder because it would be a rare exception that would require a lotta programming to get around and present properly, not to mention numerous calls for "Why can't I do this with this wood?" But, if you were interested in somewhat less exotic wood, such as Alder or Swamp Ash, it's possible they could still make the top out of one piece and thus be able to recess those knobs without it looking strange. I don't speak for them, though, so you'd have to call to find out for sure.
Body woods are not as influential on electric guitar tonal character as many believe anyway, so it's not really a performance issue. it's just aesthetics.