I have both paid versions and I haven't noticed this behaviour. I usually open my file browser, choose a book and then an app. The files stay where there are. Bookari shows a message that the book has been imported, but I think it means just the metadata and cover to display in the Bookari library. There are no duplicate book files in any folders on my internal storage. In Moon+ Reader you even have an internal file browser which you can point to your location of choice.
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