I used to have a lot of problems with font embedding automatically. Some fonts in a certain font family (even Google Fonts) have their name declared inconsistently, and Calibre had difficulties finding them. I managed to manipulate these font properties and they are imported with no problem at all.
Another workaround without "fixing" the fonts is to embed them manually. I always have Editor to arrange files into folders, though I'm not sure if they mean something to readers.
Not all readers in Android understand (properly) embedded fonts. Moon Reader sometimes display them nicely, while in other books it ignores completely. FBreader and Google Play Book are the two application that support embedded fonts more than others, as far as I can see.
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