As @SeasidePokemon mentioned, there will never be an official source stating that extra copies were retained rather than being destroyed.
This thread addresses Pkonno2002 sales, which are almost assuredly extras.
Pokumon (a highly reliable source) also addresses Pkonno2002:
However, there have been “extra” copies sold by Yuichi “pkonno” Konno, an employee involved in creating the original rules for the Pokemon TCG. Below is a snapshot from June 2020 of him selling a copy of the card. Konno has sold 2 copies so far, and both have been authenticated by PSA as authentic.