this sounds very valuable, but doesn't appear to be available through the api yet. you might consider contacting github support to request making it available through the api. if you learn anything, please update this issue with the new info.

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?

For anyone who comes here looking for this, please feel free to +1 the API feature request to help push it along:

https://github.community/t/support-autolink-reference-configuration-in-the-api/14614

GitHub Support Community

Support autolink reference configuration in the API

The Autolink References feature is very useful, but only configurable at a repository level. Since there’s no org-level support, this makes it very difficult to use/keep up to date for multiple links (such as to support multiple projects in JIRA) across all of an org’s active repos. There’s a suggestion for enabling it at the org level - but allowing us to update the list of links via the github apps API would solve the problem from a different angle, and would allow us to automatically keep th...

The REST API supports autolinks now: https://github.blog/changelog/2021-08-02-apis-for-autolinks/

The GitHub Blog

APIs for custom autolinks to external resources

APIs for Autolinks