You're missing that it is dating the material you ise to refill, not the refill action itself. You can refill with topsoil, which woild indicate EOL as you say. or you could refill with dirt from a pit, which could be thousands of years older. You could use dirt with dinosaur fossils in it, but that doesn't make the site 65 million years old.

Anyway according to other comments apparently they used a few means of dating already.