Yes, I mean Presentation MathML (I don't think Content MathML is applicable in the ebook context, since it's designed as a medium for human reading). We did a piece about the whole can of beans back in April: http://lwn.net/Articles/440313/ .... Unfortunately (though probably predictably) the comment thread eventually devolved into an argument over the abstract virtues of different approaches.
If you ask me, ultimately writing mathematics is always going to involve ambiguity -- just like writing language -- thanks to context and the brain, so debates about devising the "perfect" form of content markup are similarly moot.
Another question entirely is whether a text-centric app like Sigil is the right application to do something as layout-driven as a scientific work. I'd probably use Scribus for that; it already supports "render frames" for content in other formats (TeX included, as is gnuplot, lilypad, and a few others).
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