If you were using a 6mm endmill but probing X/Y as if it were a 1/4" endmill (i.e. 6.35mm), you’ll just be off by the difference in radius, yes? If you just use an incorrect hard-coded endmill selection to probe, jog the difference in radius, and set zero, you’re good to go, yes?
Personally, it seems as if a “choose your own diameter” option in the probe endmill selection would be all but trivial from a UI design perspective (and trivial in code), and it would tremendously improve the user experience for a significant subset of users. At least with a simple “jog the offset” workaround, it’s only an unnecessary annoyance to all our properly SI-compliant users.