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Kobo Metadata uses the ISBN as the identifier when downloading metadata. Since it only shows in the Book Details view, I personally don't find it that annoying. The IDs list navigator if you mean the dropdown menu when you want to enter an ID in the Edit Metadata view was created by @davidfor long before Kobo Metadata was created.
When I click on Kobo Metadata in the Book Details page, it opens a Kobo page for that book in my web browser. Have you configured the Kobo Metadata plugin for country and language? When I set my copy to France and fr, it opens the book page on Kobo France if the ISBN exists there or it opens an error page if it doesn't. Images of sample page opened and Kobo Metadata configuration page attached.
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