At the tax counter at SJO is a sign showing the components of the $29. It's made up of four different fees, but none of those are included in your list. (The tourism tax has existed for years and it has always been included in the price of the ticket.) I'm sure you'll have to pay upon departure.
This is so typical of Costa Rica: Announce a move with big fanfare, and then not be able to implement it. I should have known.