Given the source code for the build engine, which was ported to the N64 and used to make the game, is freely available for non-commercial use, could it be used to map some of the function and variable names?
I don't think that's what they did. Looking at some gameplay footage on youtube, it's a third person game with a full 3d player model, not flat sprites, and the level geometry seems to be full proper 3d without the build engine distortions when looking up and down. I think they built or used a different engine designed to take advantage of the N64s graphics hardware.
Something around that, they used the build engine as a starting point but "hacked it to oblivion". On the very least it reuses the same level editor (maps are vanilla build editor compatible) and it does keep many of the old bugs, like "killer doors".
semi random source: https://forums.duke4.net/topic/9513-release-zero-hour-resour...
incidentally the predecessor "duke nukem 64" is already more akin to what gzdoom is by using polygons instead of 2.5 rendering for walls and floors and they decided to push for polygons in the actors too for "zero hour" release.
perhaps with a bit of luck you'd get some useful markers / functions mapped tho, its not unheard of.
problem in my mind (didnt test it ofc) would be that the decompiled version is decompiled from a different ISA that build usually compiles to, so the decompiled version in my mind would look totally different. (you dont have the ported sources i suppose, only the originals).