You say "e.g. Sony" -- are there other e-readers that won't display an epub that's a single file?
I rather like having Sigil break my book into multiple files, since it's so easily done and doesn't seem to cause any problems, such as pointing the toc or a footnote to the wrong place. But it does seem rather odd, given that since 1991 I've had a word processor that can so easily handle an 80,000-word book without choking (WordStar 7D).
(Speaking of WS7, there's a chap building a clone called WordTsar that will run on 64 bit Windows 7 and beyond. Perhaps I can delay retirement for another ten years!)
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