Interesting. Few thousand GL draw calls does not sound too bad in general but considering how EDuke probably uses pretty outdated GL stuff and apparently does not sort calls it makes more sense.
While the original Doom code is surprisingly well designed and easy to read, Duke 3D is
a bit of a mess. It has always been fascinating how smart people deal with complex problems. Some can turn difficult problems into sophisticated but simple mental models leading to designs that are easy to reason about for others. But if you are smart enough to handle a very complicated design with a lot of mutable state in your head that might work too. It's just a lot more difficult for other people to contribute and fix issues. And after a while even the smart author who once understood everything forgets and the code becomes a maintenance nightmare.
Working as a programmer it often seems that some people, especially juniors and managers appreciate complex solutions more than simpler ones solving essentially the same problem. And arriving to the simpler one might actually require a lot more work. Carmack's solutions were often quite easy to reason about while groundbreaking at the same time and I think it's big part of what makes someone an excellent programmer.