I can definitely see why it's a difficult problem (unlike id tech stuff). As I understand it, build cames come in two parts. The Build Engine and the game module (which btw is how eduke32 is "GPL," only the Duke3D game module is GPL). The game module simply calls rendering functions within the build engine, but otherwise can be completely separate code bases. The build engine doesn't even provide sound so all of that can be cluttering up the unknowns.

Would definitely love to see more of the games supported by eduke32 though. Even if the shared code between them is minimal.
Compare that to id tech where companies were provided the source to Wolf3D or Doom to build their game upon. Overall the structure of the game is the same. The Wolf3D engine is a little harder to trace since it has more numeric constants, but at the same time, it's a much smaller code base.