"How is that possible? I could be wrong, but weren't the kick panel holes punched in different places according to production date, production plant, etc.?"
No, Original OEM Ford Kick panels had pre-punched "bossed" holes already there. The very earlier Kick panels had three screw hole bosses, and the later ones only had two screw hole bosses. The newer Scott Drakes ones are just like the Original OEM Kick panels, but a bit thicker..as the originals were like paper thin. If you have a deluxe interior, You'll still have to make those holes for the bottom carpeting and trim.
"I was under the impression that it's rare to see two '65-66s with the kick panel screw holes in the same place. Maybe I'm wrong on this one?
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Yep.
I ordered two pairs when they first came out for both of my convertibles. Excellent quality! I highly recommend them!