Not familiar with the Sig kit, but if you are concerned you can add stiffening ribs lengthwise on the cut ribs. I'm guessing you are taking no more than 1/2 the height of the rib away for the servo cut-out. You're going to have to add a couple basswood or spruce stringers to screw the servo down into anyway (aren't you?), and they will add strength too.

If it's in the center section it will be inside the plane and unobtrusive, so flush is not critical. Are you setting it flush just to clean up the cockpit for inside static scale appearance?