The main reason for the links on the front end are SEO. Of the links you mentioned only those on the page in the repository will be seen by search engines. At most you're getting two links from a single page, albeit on a very strong domain.

If your link appears on the site itself then it could generate hundreds or thousands or tens of thousands of links.

I don't mind if the front end links are on by default. In many cases the links are the only reward a theme or plugin author gets for their work. However, they do need to be easy to turn off for the average user. Something as simple as a text box or checkbox in the theme or plugin admin panel. No one should ever be forced to display credit links.