Hi there,
In the 6 years+ that GeneratePress has been listed on WordPress.org it has always complied with the WordPress rules and guidelines.
The rules clearly state that affiliate links are not allowed:
https://make.wordpress.org/themes/handbook/review/required/#selling-credits-and-links
We can categorically state that we have never used affiliate links or added code that filters 3rd party plugin upsell URLs in our Theme.
Although Plugins are not bound by the same guidelines the same applies to our Premium plugin.