Since the Kindle system fonts cover all Unicode superscript numerals (⁰ ¹ ² ³ ⁴ ⁵ ⁶ ⁷ ⁸ ⁹ *), which don't affect line spacing, it'd would be theoretically possible to replace regular superscript numerals with their superscript Unicode equivalents. However, since the glyphs for 1-4 and 5-9 are apparently provided by different system fonts, this would only work for single digit footnotes or maybe multiple asterisk footnotes.
IMHO, this would be overkill since the number of non-KF8 compatible Kindles is most likely negligible and there are far worse compatibility issues.
(The test file was compiled with Kindlegen 1.1; the source files are embedded.)
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