With Kobe ereader there are no ligatures for Kepub so I use Epub when there aren't images or notes. Otherwise I use Kepub. This is reason why with kepub I use fonts that fit good also without ligatures like Bitter, Lexia Dama or Roboto Serif. Or I read them with Koreader so I have great typography, the choice of sharpness of fonts, pop up notes and images enlargement (and many other features).
About otf fonts: if You use the patch "Enable advanced settings for all fonts" it works only with ttf font with Epub, it doesn't work with otf fonts.
I don't know any way to have discretionary ligatures but using css:
Code:
font-variant: discretionary-ligatures
I don't know if it works with epub in Kobo (may be epub 3?) It should work with Koreader.