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Quite a few of the books I've created have footnotes (eg the Rider Haggard books tend to have a lot of footnotes). What I always do is move them all to the end of the book, and create a hyperlink from the reference in the text to the relevent footnote (although I suppose "endnote" would be a more accurate term). On the Sony version of the book, the footnote you jump to might be half way down the page; on the Mobi version, the text you jump to is always at the top of the page.
As you say, for chapter links, etc, where you want to be at the top of a page anyway, there's no difference.
That's why, though, when you add new books to the Sony it grinds away for a minute or so when you first open the book, or first select a new font size - it's paginating the book. Mobi devices don't do "real" pagination.
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