DOSBox allows the ORIGINAL game to be run, so allows GOG to sell what they are advertising.
eDuke32 is a replacement engine, it is not original, and gives functionality which is not original, such as the high res pack, 3D models, lighting effects, improved mouse look, etc.
BTW AFAIK eDuke32 does not replace any game elements, so the game files are not altered in any way.
So GOG would still distribute the original copy, just bundled with additional
software, like already mentioned DOSBox or ScummVM, to run it.
I emphasize additional as this should not in any case replace the original game and it's ability to run under DOS environment, but a checkbox in installer that puts everything together (like in one single folder as it does now with DOSBox) without any need of unwanted search and downloads would be well appreciated I guess.
P.S. I use many DOSBox references here, but ScummVM is much more way closer/similar to the subject.