I rarely mix up fonts in ePubs, for a simple reason - it's hard to line them up if one needs this.
So, yes, it's the main font - and I embed it only because I need to be sure all non-ASCII characters are correctly displayed.
The method I use is to do the book, and at the end, to do the font embedding - using the calibre's own macro/function.
After I check by sampling whether the letters are OK, I do the subset. Sometimes, calibre adds a second font definition (the first being added during embedding).
I am still investigating this behaviour. What I did in the past was to have the fonts.css and the fonts renamed as calibre does in a special directory and to import both (or all of them, should they have different names for each format) in ePub.
I know that most issues are related to improper addressing the fonts.
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