Pat, doesn't making the bow center and handle center the same place, assuming a 4" handle, make the arrow pass 2" above center? Maybe I'm not understanding something correctly.
I make my bows with a shorter bottom limb. How much shorter depends on the length of the given bow. If the bow is 64" nock to nock, say, I'll measure up from the bow's center 1 1/8" to locate the top of the handle and shelf. Then measure down from the center 2 7/8" to locate the bottom of the handle, making it 4" long. This makes the center of the handle and center of the bow offset by 7/8". It also makes the center of the bow close to equidistant from the fulcrum points, or centers of areas of pressure, of my bow hand and string hand. Bow hand pushing from slightly below bow center, string hand pulling from slightly above it.
I don't 'cut-in' shelves on my wooden bows either, but rather, build them up with leather.