If you want to use calibre to download metadata but not to manage your ebook library, try using `fetch-ebook-metadata` to download metadata and output as OPF, then use `ebook-meta` to save the metadata to the book.
It shouldn't be too hard to script it.
Or just use calibre and let it handle
everything. Your choice.
If you want, you can even use save-to-disk to export a copy of your library that looks exactly the way you like it, whatever that may be.
calibre, by design, requires exclusive control over the in-library copies of your books, and needs to be robust against bad filesystem design across three operating systems, including Windows (

).
The truncated filenames are a hard requirement and will not change. The issue has been brought up before, trust me. See the above-mentioned sticky thread.