In terms of CPTUI specific settings, we have two total that we save to the options table.
cptui_post_types
cptui_taxonomies
These two hold all the selected values you choose when creating a post type with our plugin.
Everything else, posts in the post types, meta data on those posts, terms created for the posts and taxonomies, etc. They all go to the appropriate other WordPress tables. We don’t store anything like that in a custom place. We also do not delete content if you happen to part ways with CPTUI. If you delete our plugin, those post type posts will still exist in case you want to keep using them but not our plugin. However, for notable reasons, you’d need to re-register them some other way. We do have functionality to help with that if you decide to. It’s located in the Import/Export page and the “Get code” tab.