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Someone will correct me if I'm wrong but, to the best of my knowledge ...
When you open a book the Kobo checks its database for an entry for that book in the content_settings table (stores bookId, font family, size, alignment, line-height, left/right margin plus some other fields). If there isn't an entry then the settings in the config file (.kobo/Kobo/Kobo eReader.conf) are used instead.
An entry in content_settings, is created for a book when the Aa-font-icon is pressed from within that book and at least one of the sliders and/or buttons is pressed. At that point all the slider/button values are stored in the entry.
For a standard epub, the bookId is the filename. I'm not sure what kepubs use for bookId.
... so your plan of nudging a font slider left&right for each new book, to 'set' the per-book values should work, I think.
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