Change WordPress user roles and capabilities › Forums › Bug Reports › Custom Post Type Capabilities – Multisite per-site? › Reply To: Custom Post Type Capabilities – Multisite per-site?
Currently, the only way is to network deactivate User Role Editor Pro and activate it for selected sites separately. Then you will have separate “Settings->User Role Editor” menu for every site and separate set of URE Pro configuration options.
May be I will add with one of the future updates a custom filter which allow to change option value via code.