Press Permit’s functionality is different from and complementary to a basic role editor / user management plugin. In terms of permissions, those plugins’ primary function is to alter WordPress’ definition of the capabilities included in each role. In other words, they expose lots of knobs for the permissions control which WordPress innately supports. That’s a valuable task, and in many cases will be all the role customization you need. Since WP role definitions are stored in the main WordPress database, they remain even said plugin is deactivated.
Press Permit can assist you in turning the site-wide capability knobs for desired post types. But it also supercharges your permissions engine. Press Permit it is particularly useful when you want to customize access to a specific post, category or term. Extension plugins add collaborative editing control, file filtering and other features which are not otherwise possible. The plugin will work with your WP roles as a starting point, whether customized by a role editor or not. Users of the PP Collaborative Editing extension can (after activating advanced settings) navigate to Permissions > Settings > Role Usage to see (or modify) how Press Permit is using your WP role definitions. Press Permit’s modifications remain only while it stays active.
July 2012 update: see Capability Manager Enhanced.