MightyKhan: not sure how they do it, but the developers are masterminds when it comes to coding/hacking..
I believe the means of doing so was planned to be through the same manner in which we do our engine hacks, by hooking the executable and redirecting to custom C++ functions outside of the game, similar to how NWN Refreshed appears to be handling it. Needless to say if NWN Refreshed is released in the near future it will save Acaos a good deal of development time.
While the PRC is likely the only source for new base classes at the moment, working around the engine in order to implement those classes does cause the result to be less streamlined than vanilla NWN...but if the added classes are all you're concerned about, the hoops you may have to jump through to use them could be acceptable.