The answer is rather simple, actually. It's all about subtracting material and sculpting the wood. With a wooden flute, the tone hole is cut out of the body in a process that is referred to as "milling." However, after the tone hole is milled, more material around the hole must be removed to allow clearance for the key cup. Since it is a wooden body, you are actually carving or sculpting the wood to create the convex shape around the tone hole. The tone hole itself has a flat edge, so the key mechanism functions exactly the same as it does on a metal flute. The key cups and pads are exactly the same size and shape as those on a metal flute -- and they cover the hole exactly the same way as they would with a metal flute.
But what about the rest of the body? Is it the same thickness as metal? Obviously, no. A wooden flute body is thicker than a metal flute body. The wood has to be thicker so it doesn't crack. However, the inner bore diameter of a wooden flute is exactly the same as the inner bore of a wooden flute. So, there are some differences with the wooden flute but many more similarities.
|Wooden flute bodies before and after tone holes are cut.|
|Close-up on the tone holes (notice carved covex shape around hole for key clearance)|
|Final assembly with keys in place.|