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My experience with ereader books is that some of them apparently "just work" because they don't use any of the offending characters: they use three periods instead of an ellipsis character, a hyphen instead of an em-dash, etc. I think it has more to do with the way the individual book than the fact that it comes from ereader.
I'm not brilliant with character encodings, it's not something I deal with often in my programming, but I would think that if we put in a function that would detect and replace unusual characters with their character entity encodings (for example, ampersand rsquo; for a right single quote) it might work a lot better. (I had been doing a little of this manually to make my books work better and was going to write a short program to do it for me, but am not going to bother now that I see that I can do it from the command line and it works fine.)
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