Instead of getting the fpurl and passing that to zencoder via a $.ajax call, first pass it to your server and then hit zencoder server-side using one of their libraries.
(I'm not trying to be down on what has been developed here - just trying to understand how it is different from what was already possible)
It seems to me that most of the FilePicker documentation talks about using it in client side applications ?
Because we're so heavily client-side, we created a policy-based security api to allow you to control the actions allowed using the filepicker.js library, as well as actions in your developer portal that you can use to make things read-only, set the max allowed file size, etc.