First of all, I'd like to commend you on this outstanding remake and the work on rend2. It looks fantastic and actually motivated me to map for JA again after more than 10 years.
Could you elaborate a little more on the process of generating the lightmaps, specifically the HDR ones? You wrote you are using Blender for this, correct? Looking at the PK3 you released, it seems the .hdr files in the maps folder contain the baked lightmaps. I guess q3map2 cannot generate these. But then I am asking myself, how the lightmaps are compiled into the BSP. A decompiled version of your map at least revealed some q3map2 parameters being used. It seems you are combining the Radiant BSP with the Blender BSP using the -mergebsp switch.