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I believe you are misunderstanding how FanFicFare(FFF) works and what it's for.
FFF doesn't download any of AO3's ebook formats, FFF downloads HTML and generates its own ebook format files.
The recommended output format for FFF is EPUB because that is the one format that FFF supports updating. The other output options are honestly only there because they already were in the code base when I came to project.
The primary use case for FFF (IMHO, at least) is to download updates to stories you are following with the first secondary use case being downloading new stories.
I read on Kindle myself and use Calibre's Convert feature to make AZW3s from the EPUBs and side load them using USB.
Although you apparently want to convert AZW3 to to EPUB anyway? I don't know what all that is about.
You mentioned 'bulk download'--I generally recommend against doing large numbers of downloads at once from any given site because many of them have mechanisms that will detect that and throttle or block your access to the site.
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