The person Rusty asked said it was applied with the black plate in the first run and there were two black plates,
one for the 1st edition and one for the unlimited (shadowless) run.
Here´s a visualisation of the two black printing plates at the example of Venusaur:
http://i1230.photobucket.com/albums/ee481/darkrai_star/BlackPrintingPlatesVenusaur.jpg
But that´s contradictory to the answer that the stamps are applied separately. So my idea is,
as the 1st edition printing plate was destroyed after the first run and they didn´t want to
reproduce it, they decided to add another printing step to the printing process where the stamp
is applied to the cards afterwards, so they can reuse the same plate with just the stamps for
every upcoming set.
What do you think?