Yes, so the section that psychopath quoted has to do with cases when part of the program itself forms the output generated. I think none of us here are familiar enough with Q3Radiant and Quake3 BSP files to say something conclusive about this.From my understanding of it, the anti proprietary / anti drm section is focussed on excluding drm / proprietary code in gnu-gpl software, not on making output fall under the gnu-gpl.
I suspect that if templates are used here, they are just input data for Q3Radiant, so the output would not need to be licensed under the GPL.