Yes, you can definitely have a combination of free ad listings and paid ad listings, but in terms of the specific questions you asked, no the theme will not do this by default.
Advertising spaces are totally separate to normal ad listing spaces, and other than the advertising space you see configurable from the
ClassiPress admin demo (see the "Advertising" tab), you could manage any 125x125 sidebar ads using a plugin if you wanted to.
I don't know what you mean by "content outside the theme"? But if you're basically talking about customizing the theme, then yes you can make changes, our themes are not encrypted so you are free to make changes as you wish.