Long story short: Paramount's "$94 million" budget, thanks to various international tax breaks, merchandising deals and the like, was actually more like $7 million. Read more here. Of course, from a studio accounting point of view, that $94 million was almost certainly the 'official' figure when it came to dishing out net, rather than gross, profits.
Well, yes and no. The movie did cost $94 million dollars, in terms of a production budget, but you're right in bringing up that article that points out that merchandising, tax breaks (Uwe Boll is famous for exploiting the German tax break on his films, although, for all the crap he produces, he ironically is one of the few using the law in the spirit that it was created for), selling television rights, and selling overseas rights helped to cover most of that cost before production began. It's no surprise to me that studo lawyers obfuscated this information in order to reduce the ammount of money they'd have to pay people for its success.