What jackie_w says is how I understand the font settings are handled. When you make a change to the font settings, they are written to the config file and a content_settings row is created or updated for the book. If there are no stored settings for a book, then the settings are read from the config file.
These rules don't change for the different formats. epub, kepub, text, mobi, etc all use the same settings mechanism. They don't all use all the settings, but the basic mechanism is the same.
I have just done some testing with a few epubs and sideloaded kepubs. The settings are being saved as described above into the database and config file. And opening a new book will always use the settings in the config file.
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