Yes, setting options are different when you read PDF files and EPUB files.
When you are reading EPUB files, changing font type, font size, font and background colors, margin, text alightment, line spacing, brightness, orientation, tap mode and screen timout are available under Settings.
When you are reading PDF files, changing brightness and orientation are available under Settings. To change the font size, you can use pinch to zoom gesture. For more details, please look at here: http://aldiko.zendesk.com/entries/390575-how-can-i-zoom-pdf-files