I've tweaked the under/surface warp slightly to be more robust. This won't affect the scaling of it though.
I can see only one possible way for that weird colours quad, and that requires drivers which don't follow glsl specs properly where errors are concerned. The error in my code is fixed so should now use slightly better tested pathways through your drivers so will hopefully work properly now, but no guarentees.
lighting-wise, q1 vs q2 comparisons are mostly down to the tools rather than the formats.
I'm sure someone could fairly easily write a radiance tool for q1 bsps also (using .lit support), I'm just not aware of any real public version of one though I am sure there have been such efforts in the past.
q3map2 probably has even nicer lighting though, but this requires q3bsp/rbsp/fbsp so would be noticably harder for software renderers to implement. To be fair, its enough work for gl-only q1 engines too, such that widespread support is unlikely with either q3bsp or q2bsp regardless of whether its a software engine or not - especially if your mod has other dependancies/requirements also.