There are a number of factors in play here. There are the dimensions of the embouchure hole at the top, but that is only the beginning. Very important is the chimney height (so called high wall and low wall) both in front and in back. Then there is the angle of the walls. The chimney is not just straight up and down, but there is a curve in the front, meaning that the hole in the flute body is actually not the same size as that at the top of the lip plate, it is larger. Some head joints also has an angle in the back wall, and some, such as the Cooper head, also have flaring chimney walls to the sides. These are all quite critical to the sound and response of the head joint, and they are interactive to some extent. So asking for the size of the blowhole is only one of a number of important measurements. The very best way to visualize this, rather than trying to take measurements with an assembled flute head, is to make a wax impression of the geometry of the chimney, from which you can take measurements of the top hole, the bottom hole, the height, angle and possible curvature of the chimney walls.
Whatever you do, make sure that there are no sharp edges in the final assembly, the only edge that should not be rounded is the top blowing edge. Make sure that the hole cut in the body does not have a sharp edge, as this will cause turbulence and seriously impair the performance of the head.