1. You may use your existing Wordpress install as Jobroller uses custom post types for the jobs listing and so it won't conflict with your existing blog posts. However, it is recommended to backup your database first before installing Jobroller just to be safe.
2. As a theme, you can only use Jobroller at a time and yes only the theme is included in the purchase. However there are commercial child themes that you may use if you intend to have a different look of the theme.
3. Please take note that official support only covers the default theme configuration while code customization for features that are not yet on the theme is community supported. It just reiterates that any additional function or feature that are not yet on the current theme version is possible through code customization. The theme is not encrypted and so it can be modified according to your requirements. Implementation is just dependent upon your coding skills or you can avail the services of an experienced coder to do it for you. Likewise, Appthemes have certified community partners
http://www.appthemes.com/partners/ that can be contacted for customization jobs.
Also, Appthemes have set up a voting system for certain features of which the implementation is dependent upon the numbers of users requesting for it at the Ideas Exchange page
http://ideas.appthemes.com/jobroller/.