And a file manager doesn’t track which books of mine are synced and which are not. Calibre does.
A file manager does not make it easy for me to correct the ebook’s metadata so it appears properly on the ebook reader. Calibre does. Calibre will also automatically download metadata for you from a variety of sources (with many options for the level of automation, including individual review with diffs from the existing metadata).
Calibre also makes it trivial for me to create a web server so I can access my books from any device from anywhere.
Calibre will also track which books I’ve read and which ones I haven’t. Which a file manager won’t.
Calibre also makes it possible for me to read the books on my computer itself before I sync them to my device.
Calibre will also automatically convert my book to a different format depending on the device I’m syncing to, something a file manager won’t do either.