I think a good way to notify site owners of new functionality would simply be to have the system account send a private message with details to the admin and maybe also post it to a changelog topic in the Staff category as part of the upgrade process. Just a short message explaining that “your forum is now upgraded to version x, these settings are new, check Discourse 2.3.0.beta6 Release Notes for more details.”
There’s no need to build a bunch of new ux for it when there’s already an excellent mechanism for linking directly to a site setting from a post like this https://discourse/admin/site_settings/category/all_results?filter=clean%20up%20inactive