A common way for me to do this and keep using the E3/A3 licences is to use a Canvas App with SharePoint lists and standard connectors.
I will do another blog post on the exact details but in summary I use SharePoint lists that have Item level permissions set so that users can only read or edit their own records. I then have a members group with designer permissions so they can read and edit all records.
The intention then is to hide away items that members shouldn't see within the app itself and generally keep people away from the SharePoint site completely.
Read the full article
https://www.thepowerpros.co.uk/post/template-how-to-write-a-tips-blog-post
But why? Because, My custom application uses some configurations which should be stored and retrieved from a SharePoint list, but it must not be visible to end-users to avoid any mess. So, we got to hide our configuration list from users.
https://www.sharepointdiary.com/2013/06/how-to-hide-list-or-library-in-sharepoint.html
Sometimes when building any solution based on SharePoint we need to hide a list from the site contents, for several reasons. The list can be creted to be used only by an automated solution and not to be updated or accessed by users. Even if we restrict permissions to read-only in the list, this can cause some confusion in users.