it wasn't like some puzzle on the back of a cereal box either, it stumped a lot of people
It wasn't like an "in your face" "we got a puzzle on this album, buy now to try and figure it out!" No one would know there was a puzzle to it unless they were already a hugely obsessive Tool fan to begin with.
They made the puzzle for a small audience of people: their bigger fans.

That's what I like about them, they're willing to give back to the fans more than what's expected of them.