Is there a way to integrate revisioning with Panels + CTools content types?
Unfortunately, I can't think of any simple way to do what you want.

I would probably have solved it by having the content type pull it's content from the entity they are displayed on instead.

It's possible that fieldable panel panes could be useful to you.

In the end, if you really need revisioning on the the content type settings form, you're gonna have to implement it yourself. Since the form is a standard Drupal form, I would try doing it with a node type as backend, instead of doing the whole thing from scratch. You should be able to just load up the edit form for a node, and re-use most of the functionality.