"The retaining hole (was) there for a reason."
Yes but that reason was sensible only with the Modolo "pro" style holders which use long bolts instead of these "Sporting" and perhaps "Flash" model holders that have a stud which appears to be unnremoveable and nuts that screw over the external ends of the studs. These Kool Stop pads were not designed to work with such holders and they don't, unless you resort to gross modifications.