Hi Andrew,
My spontaneous answer is that it will not be possible since we want our end consumers to be able to use their EyeX Controller with more than just one application, and we want them to have all the benefits of a centralized handling of the user calibration profile and screen setup (for example not having to re-calibrate for every app they are using).
But if you think you have a good business case here you could try contacting someone from our partnership program and see what they have to say: http://www.tobii.com/en/eye-experience/support/contact/isv-contact-form/