That’s right. Here a close-up of it from my 1st edition stamp variations article:
You’re indeed correct that those were printed with the sheets and the stamps were placed on top of it. Sometimes this is slightly misaligned, causing the 3D effect:
As apposed to a 2D effect:
In my experience, the 3D thick stamps are actually more common to find on (non-holo) 1st edition Base Set cards than 2D stamps, although not by much. Probably 60-40% distribution if I had to make a guess.
Yes, this misprint only occurred on Pikachu, and could come from Shadowless ZAP! Theme Decks with the gold strip around them (here an example of such a Theme Deck opening with four of these Pikachu).
Greetz,
Quuador