Can I ask questions about non-default Drupal core modules or themes, on Drupal Answers?
Yes, you can.
Questions can be about any Drupal module and theme, both the Drupal core one, and the third-party ones you find on drupal.org; it could be also a question for a custom module you created. If you are asking about a third-party module (or theme) that you find on drupal.org, I would suggest to report a link to the project page.
Keep in mind that you could be asked to show the code you are referring on the question; if you are not willing to show the code, the answers you get would be too generic to be useful.