Breadcrumbs not consistent with Permalinks

I’m using wpgeo paid version for a client.

In order to achieve more control over the permalink structure we have each new type of listing as a custom post type. The system however forces us to use a category even though this is not needed or wanted.

Breadcrumbs do not conform to the Permalink structure set.

We have:

mydomain.com/post-type/region/city/listing-name

When clicking /region/ or /city/ in the breadcrumbs we get error pages nothing found I expected to see a listing page of listings from that region.

Additionally I find no way to display the available post types if there are multiple types to allow users to see number of listings per type as there is for category of post type. Is there a widget or something for this?