When you install Moon+ Reader or other app do you in its settings tell it what folder on the SD card your books are in? That is the "Main Folder" setting in Moon+ Reader "Options", for example.
I've checked a few things to be sure -
With Moon+ Reader installed and the above option set and opening books in that folder it definitely does not create a copy of the file in the device's own memory nor anywhere else when the book is opened from Moon+ Reader.
Also, if I put a book in any other folder on the SD card (i.e. not the folder that is set in Moon+ Reader's options) and browse to it with a file manager and select Moon+ Reader to open the book from the choices offered, as you say you would like to do in your first post, it again does not create a copy of the file anywhere (not even in the "Main Folder" set in Moon+ Reader's "Options" , it uses the file pointed to with the file manager).
Now it might be, but I would have thought unlikely, that if you install Moon+ Reader (and other similar apps) and if you do not tell it the "Main Folder" for books in its setting "Options" that if you navigate to a book on the SD card with a file manager and open it and choose Moon+ Reader that Moon+ Reader will automatically create its own default "Books" "Main Folder" in the default position, which is in the device's memory not the SD card, and put a copy of the book there. But I have not tested that as in order to do a fair test I would need to completely uninstall my exiting setup.
I have used Moon+ Reader and PocketBook extensively on three different devices (2 different model Samsung tablets and a Sony Xperia phone, covering Android 6, 7 and 8 devices) and have never had the behavior you describe; but have always been set up with the "Main Book" folder set in "Options". I have occasionally tried other reading apps in order to choose my preferred ones and have never noticed any behavior different with them either.
If after all that you still have the same problem then as LucyOne suggests there may be something strange with the way your device handles files on SD cards in the circumstances of using a reading app.
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