JTC ONLY effects users (Administrator, Editor, Author, Contributor, Subscriber) that are logged into the site. The logic is that if you are allowing users to post comments on your website without creating a user account and logging into your site to post comments then you obviously do not care about getting spam comments. The only way to control comments is to require that users create a user account and login to post comments.
Comment Form: (only applies if Comment Form CAPTCHA is enabled/checked)
Enable|Disable JTC Anti-Spam For These Registered/Logged In User Roles:
Users must be logged into your website for the Comment Form User Roles to work. If you do not require that users are registered and logged in to post comments on your website then these JTC Anti-Spam options will not have any effect. These options are ONLY for registered and logged in users and ONLY for your Comment Form if you are using this WordPress Discussion setting: Users must be registered and logged in to comment.