I am having problems finding details about publishing an Add-in to the office store. I have found this but it does not provide details on how the publishing works. Does the store just store a catalog for the manifests? Or does it host the html, js and other files too?
The resource you have found is correct one and describes step by step submission process. You also right that the Office store is the catalog of the manifest files, which pointed to web applications. You have several options how to publish your application described in Deploy and publish your Office Add-in. To have better picture on the topic you may read the following document: Components of an Office Add-in. The picture below should be the answer on your question ...