1. The intranet configuration wizard doesn't affect folders, the file structure or other your data; the only change will be that there is a new view that is different from other previous templates.
You can try this template if you have a test installation.
2. There is no step for choosing the template in the extranet configuration wizard now. If you run this wizard, your extranet gets the same template as the intranet. This is related to our new concept:
company employees no longer have to go to the extranet site to communicate with extranet users, it is possible to work with them right from the intranet (of course, within workgroups marked as extranet). So there is no need to divide extranet and intranet in their appearance, as employees need no longer need to worry about which ‘side’ of the product they are on.
If you apply the Social Intranet template to the intranet and run the extranet configuration wizard, then the extranet will have this template. You can apply the previous template to the intranet later.