That's correct. in ArcGIS Online My Content choose Add Item > An Application, and use the default Web Mapping option. Enter the URL to your self-hosted app, the app title and tags. It really helps if you add 'story map' and the name of the app you used 'map tour', 'shortlist', etc into the tags field so people can find it if they search for examples. Then press Add Item and you'll have a web mapping application item representing your self-hosted app. Upload a nice looking thumbnail, add any other descriptive text, then share it.
Adding web mapping application items manually into ArcGIS Online enables your self-hosted story maps to be discovered when people search ArcGIS Online and to be added into galleries. For example all the self-hosted examples in the Story Maps gallery have web mapping application items created for them, which is how we were able to add them into that gallery, the featured story maps on the Story Maps home page, and into the gallery on the ArcGIS Online website.
Note: web mapping application items you add into ArcGIS Online manually don't show up in the My Stories tab on the Story Maps website. My Stories only shows you your hosted story maps in ArcGIS Online and ArcGIS Online of course automatically generates web mapping applicatin items for all your hosted story maps.