How to generate a foolproof polytonic Greek ePub for the Kobo?

Question

I intend to use Seumas MacDonald’s Ἡ Ἑλληνικὴ γλῶσσα καθ’ αὑτὴν φωτιζομένη (Lingvæ græcæ per ſe illvſtrata, or The Greek language illustrated by itself) to learn ancient (Koine) Greek. I can load a PDF nicely in my Kobo. The ePub loads too, but does not show accented characters. I opened issue #19, https://github.com/seumasjeltzz/LinguaeGraecaePerSeIllustrata/issues/19 in the project, and there I documented my fiddling; to sum it up, I had to load a polytonic Greek font in my Kobo and alter the ePub generation script to point to that font. Now, what would be the canonical way of doing it? I guess there should be a way to generate an ePub file without specifying any given font, but so that it automatically uses a font with the glyphs needed if it is present in the reader.