In reply to Jack.

The plugin and theme directories are run by two different groups with two different sets of guidelines. What plugins are allowed to do is different from what themes are allowed to do.

There is certainly an argument that some of the guidelines should be shared across teams. Affiliate links would be one of those things. Because such links are not specific to theme or plugin development and can occur in either, it makes sense that there'd be a unified WordPress.org guideline for addressing them.