There never was the ability to open Clippings Manager from extension preferences in previous versions of Clippings. That said, it certainly can be done in a WebExtension. I will consider adding this feature if there is significant user interest.
All those permissions are needed for Clippings to function. Go to the following page to learn more about the meaning of those permissions, and why they are needed: http://aecreations.sourceforge.net/clippings/permissions.php