URE Pro does not support wp-cli and any other CLI commands. If URE Pro is involved, You may temporally deactivate it – just rename it’s folder /wp-content/plugins/user-role-editor-pro to something other. It will be executed and will be automatically deactivated on ‘Plugins’ page opening.
URE Pro stores it’s settings in the database:
SELECT * FROM wp_options WHERE option_name='user_role_editor';
So you may change URE Pro settings replacing option_value field value.
For example, find
and replace the final 1 with 0 in order to switch OFF the option “that CPT use their own permissions”.