When you change the font setting when reading a book, it saves the settings for that book. It also saves the settings as the defaults for any new book that you haven't set the fonts settings for. This means any new book you open will get those settings.
The settings don't override everything in the book. For kepubs, the font should, but, the size is not an absolute setting, but, a relative setting. That means if the styles in the books sets the font size to different things, then the font size you see when you open the book can be different. I tend to clean up the fonts if the book does something silly. That's basically removing the font size for the "normal" paragraphs and making sure everything else uses "em" as the size so they are relative to that. With that, I don't need to adjust the font size when changing books.
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