Well, as they’ve implemented their plugin, perhaps that is true, but as I stated, by registering a post type differently, you get a permalink like you want. Apparently with that plugin such a registration is not possible. If you were to register your own post types instead of using the plugin, you’ll find that is the case. Such custom code isn’t too complex in itself, but deciding on the right parameters can be confusing. Going with the defaults often suffices though.
Another possibility is creating your own rewrite rules. Depending on how many post types you have, the rule may end up being rather complex. There’s no reason you couldn’t add several rewrite rules if that somehow made more sense. The crux of custom rewrite rules is arriving at the proper regexp that matches your permalinks, without erroneously matching other permalinks that need to be handled elsewhere.
The other side of the custom permalink equation is getting WP to generate permalinks in the proper form. The solution is theme dependent, but most themes use the default WP functions. In that case, use “post_type_link” filter to cause the generated permalinks to be the format you want.
When you change anything related to permalinks, you need to flush the rewrite rules to get the new permalinks to be recognized. For your own custom code, using flush_rewrite_rules() isn’t necessary, it’s a very resource intensive operation that doesn’t need to be repeated until another change occurs. I recommend instead manually triggering a flush by visiting the permalink settings page. This happens automatically once you leave the page. It’s irrational, but I feel better clicking the save changes button even though nothing was changed. I still haven’t gotten used to things updating automatically without needing to explicitly save ??