1) framework builder isn't used to create new designs it is used to transform dreamweaver templates to Framework Themes, which eliminates some of the drawbacks inherent in standard DW templates and adds new capabilities.
2-3) There is an option to transform all of your templated pages to the new theme when you create the theme from a dw template
there could be some conflicts with extensions that have redirects when using plugins, not themes
those conflics can be easily accounted for and are fixed in recently updated products