Permalink Manager is fully compatible with custom post types and taxonomies registered with custom code snippets and third party plugins (eg. Pods, Custom Post Type UI, Toolset, WooCommerce).
Using “Permastructures” editor you can replace original permalink settings with fully customised formats individually for each post type and taxonomy. You can remove the permalink bases completely or change them to whatever you like. Here you can find more info on how to do it. Furthermore, if have you either WPML or Polylang plugin installed and configured, you can specify different permalink formats for each language.
Each custom permalink can also be manually adjusted if you would like to define completely personalized URL addresses per post or term. A more detailed instructions is available here.