In reply to kapanther.

The Site Logo and Site Icon are actually two different things. The Site Logo will allow you to choose a logo for themes that support it. And the Site Icon allows you to create a favicon and mobile icon, regardless of your theme. You can read more about each here:
http://jetpack.me/support/site-logo/
http://jetpack.me/support/site-icon/
I hope that helps clear things up! Feel free to give us a shout if you do have any questions.