Not yet, unfortunatelly. Today, the Application Folder is hard coded to [ProgramFilesFolder][Manufacturer]\[ProductName].
In the future, there will be a "browse" button next to it and you can change it to any value.
The shortcut folder is the main place where app shortcuts will be installed. Currently hard coded to Start Menu/All Programs/[ProductName].
In the future, you'll be able to change this one as well, to whatever value you wish.