it is not broken actually, bread crumb doesn’t work in the logic you explained above, default, it shows “Home tag / category post”, so your custom ‘wpdm-all-packages’ page is not actually part of site breadcrumb, but if you want that with breadcrumb, you need to customize the breadcrumb code. But you may try enabling archive page from download manager settings and user the ‘wpdm-all-packages’ page slug for archive page.
About the url path, actually your logic not right, the package url format is “[site-url]/[package-url-base-slug]/[package-slug]”, so there is no way to put “[category-url-base-slug]”, for custom post type wordpress doesn’t work in that ways.
