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calibre by default likes to turn everything into unicode, in addition to nuking doctypes (because you can do just fine without them). For calibre, functionality is the chief goal. As a tool used heavily by endusers, this makes sense.
Sigil puts more focus on following the IDPF rules and making spec-compliant EPUBs. As a tool used heavily by ebook producers, this makes sense too.
The two objectives have been known to clash.
