The file `duk_config.h` is imported from Duktape project as it is and I would try to avoid diverting from the official version:
We had tuktape v2.0.0 and I just updated to v2.0.2. Can you try with kamailio master branch and see if all ok? I noticed some updates in the code regarding to this and may have it addressed. If all ok, I will backport.
If not, then I would suggest to also report to ducktape project so there it gets fixed as well.