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I get the impression that MathML support is still a bit wobbly, while Javascript support seems OK in EPUB3 (and iBooks, for that matter). Will it not be safer to use MathJax to display maths? And in that case, may it be preferable to keep the maths in the LaTeX format (which MathJax supports), thus keeping the source human-readable?
Of course, if Amazon/Kindle is the target, you are stuck with EPUB2 solutions. And given that Amazon still haven't solved their little embedded-fonts problem, you are stuck with displaying all maths as SVG if you wish to have consistent display of math symbols. And good luck with the proper vertical alignment of inline SVG's with superscripts etc....
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