ufo2fdk is embedded and by default using the embedded FDK, you can disable the use of of the internal FDK in the preferences.
The file menu option "Generate" or through scripting font.generate(...) is using FDK to build the binaries. It's up to you if you want to use the embedded FDK or a custom installed version on your local HD.
There is a scripting possibility to access, change and manage the input string for the space center
see http://doc.robofont.com/documentation/scripting/api/mojo/mojo-ui/ (CurrentSpaceCenter)
If you store user defaults through the app its will be fine.