Yes, straight-from-the-store Kobo ePubs are stored in a different hidden folder. And no, going there won't help you, because they are DRM'ed.
So, yeah, you'd have to get rid of that first.
Note that MathML & SVG support is minimal, so, tables, we rock at (thanks to @poire-z
), but graphs may be another kettle of fish if they're not plain bitmaps.