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Yes. On the Kindle there's just the single Home screen where all the books are listed (until you start sorting them into Collections) and there's just the one "documents" folder for all your stuff when the Kindle's mounted as a removable drive.
You can, however, create sub-folders within the documents folder to sort your physical files. It won't auto-arrange your books into Collections, but can be useful for when you want later to back up just your personal docs, or your non-Amazon books, or whatever and don't want to have to sift through the lot.
The only real distinction between Amazon-bought books and your sideloaded stuff on the Kindle itself is that only the former can be pulled wirelessly from your archives or have the notes/highlights/bookmarks backed up to their server.
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