Is there a way to make these unofficial expansion packs work with the GOG.com version of DN3D?
Yes. The GOG version just bundles it with DOSBox, so the game itself is just the DOS version. Therefore you should be able to just use DOSBox to run the DOS installers of the expansions.
Alternatively, use eDuke32. It is possible to use just the core game files and the core files of the expansions to get them running, but it takes a little bit of extra work to get the right format files (I had to search for how to do so and it involved using user-made apps to extract the files from the expansion installers).