This is due to Opera fixing things to be like (not exactly the same, but close to) other Chromium-based browsers where each profile is in its own folder where the other non-profile-specific files and folders are in the root of the profile path outside of the specific profile folders. By default, the first profile uses the folder named "Default". Others (create extra profiles in other browsers like Chrome to see) will have their own folders.
To be clear, the three relevant files (Bookmarks, BookmarksExtra, and Bookmarks.bak) can still be found at the old location
These leftovers are due to upgrading the profile to copy things over to the "Default" folder. If you start with a new profile, you won't have duplicates (old and new). You'll just have the ones in the "Default" folder.
Although I didn't test, you should be able to delete all the old duplicates profile-specific files and folders in the root of the profile path and be good. Just leave the non-profile-specific files and folders alone. And, back up everything before trying for good measure.
Not sure if Opera is done messing with things in this area though, so more changes might happen.