Hi savior,
Because libnoise is a C/C++ library, the only way you can interface with it is by scripting or coding. With Terragen I hope we've given you enough control in the GUI to do a lot of what libnoise can do, plus many things it can't.
We do plan to add scripting functionality in the future (probably with Python), although there are no detailed plans yet. Also, some day we'd like to release an SDK, and that would probably include header files to allow you to use some of Terragen's libraries directly in C or C++ code (among other abilities), if that's what you're looking for. This is some time away, however.
Matt