The $40 Criterion doesn't earn Criterion $40. That's not the actual cost to the retailer per unit they sell. Bottle Rocket CRIT is going for $28 on Amazon. There's royalty payments and production costs and distribution fees. They have to pay for that new transfer. They still have to move a certain number of copies to make up the expenses of this new launch. The profits dry up quick. Sony's version is selling for $6. Sony will get their $2 profit from each so making this deal won't hurt them.
The question is how many copies can they sell of Limited to make it worth Fox to lose complete control over their original release. Sure there is an X number of diehards who are eager to buy it. But what makes it interesting is that Fox did lose a large chunk of change on the film. If Fox thought there truly was a market for a "Criterion"-like Limited release, they could easily do it themselves - put out a Blu-ray with all the charming bonus features for a 2 disc set. But odds are that Wes won't be cooperative because he only wants his deluxe stuff out on Criterion so he can take up a couple more numbers on the spine.
It is a shame that the DVD business isn't like the CD business so we could know how many silver discs move when a company decides to let Criterion put out a version versus when they create their own 2 disc edition. Although the key to letting Criterion handle the release is to stick them with the bills for the upgrades while making sure that your profit share isn't touched.