Sorry Jon, you're wrong. You can have different settings for individual books.
When you open a new book, the font settings are read from the configuration file. If you change the settings, they are saved into the configuration file and into the database. If you close and reopen the book, the saved settings from the database are used. If you open a new book, or one that the settings haven't been saved for, the settings are read from the configuration file.
When I open a book that has set the font size, after adjusting them settings for the book, I close it and find book with my usual settings. I open that which loads the settings from the database and change the font size up and then down by one. That puts my normal settings back into the configuration file ready for the next new book.
Also, if you are a calibre user, you can use my Kobo Utilities plugin to set or remove the font settings for any book on the device.
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