The wiki post type is not available for customization because it is already customized by the wiki plugin while it is created. Thats why you don’t see an entry for it within the settings page.
Even through the capabilities are customized, they are not attached to any roles, not even Administrator role. Usually when a plugin creates a custom capability, it will be attached to Administrator role, because Administrator role is supposed to have all the capabilities. User Role Editor finds capabilities by looking at the role objects. Since these new capabilities are not attached to any roles, it fails to find them.
Your best option is to manually create these capabilities using the “Add/Remove Cap” functionality. Below is the list of capabilities to be created. Make sure you add all these capabilities to the Administrator role.
In my next version I’ll add code to explicitly look for capabilities created by custom post types even if they are not attached to any roles.
Let me know if you have any questions.