An answer:
I don't know if percentages work, but Joshua Tennent recommends that you avoid defining margins with anything other than pixels. After trying a variety of percentages and em values I finally used pixels to define my top margin values (as a text style attribute in the CSS template), and it worked on the Kindle and on Kindle for Mac - though it took some experimentation to get a value that looked "right" both on KfM and on an actual Kindle.
Percentages would be much more useful - for example, the way my title page is formatted now, you'd have to scroll past a significant amount of white space to find the title on the title page on an iPhone - but I could not seem to get percentages to work at all.
Thanks, bfollowell and jellby, for your help!
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