Hassio isn’t based on Raspbian. In fact it’s powered by Docker. Hassio is used as strictly a home automation system and, from what I’ve experimented, is useless with the command line. IMO, Hassio is a “plug ‘n’ play” option. If you want to use the GPIO pins you’ll have to install Hassbian and not Hassio. Hassbian will need a bit more TLC though. If you’re feeling adventurous and know Linux pretty well, you can try the manual install.
edit: Check out this post. I was confused when I first installed Home Assistant as well. What is the difference between Hassbian and HASS.io?