Is there a way to integrate revisioning with Panels + CTools content types? I'm using CTools content types to make highly customized Panels panes. The panes together form a Panels Node (I'm using the Panels default module for this).

The Panels node itself can be revisioned, but these revisions do not include changes to the content that lives in the panes. It seems that the content of the panes themselves cannot be revisioned.

Is there a way to use revisions/workflow/workbench/anything to control the publishing flow of the panes?
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.