Currently in order for any device to see the to see the entire desktop of a student Chromebook, Google mandates that you must prompt the user at the start of each session you wish to see them in. This means that until Google's requirements change, Vision will continue to prompt the user to share their screen. Any applications that are not prompting for the screen sharing are only seeing the browser or their own application, not the entire desktop of the Chromebook. All features of Vision for Chromebooks will activate regardless of whether they activate the screen sharing or not as soon as they connect. The only feature that won't work is the thumbnails/Live view.
If Google changes this requirement Vision for Chromebooks will be updated as quickly as possible to allow this permission to be automated as per their new policy. To read about the policy and the request to have it fixed, click here.