If I read the post right, the OP wants counterbores to be aligned at both ends of a hole on a rectangular block.
Make the first bore then using a locator of the bore size to locate the first bore on the table under the spindle. This will put the opposing surface up and the first bore under the spindle putting the second face under spindle for the alignment. Make the second bore. If both faces are parallel the bore will be aligned.
If the opposing faces are not square with each other, make the locator for the bore and long enough to locate the through hole and hold on an angle plate using a surface parallel with the hole.
My .02 cents worth.
If I'd a known I'd live this long, I'd a had more fun getting here!