Is that the case?
https://fabiensanglard.net/3dfx_sst1/ has a side-by-side screenshot comparison of the two, and software Quake's colours and lighting look way more rich and vibrant; it's not just smoother textures. It's possible that GLQuake/one of the many source ports since has improved on this though.
Of course I know this is a particular quality of GLQuake and not an actual limitation of hardware rendering. And I agree with in general with the contention that this article is talking about a particular art style associated with mid 90s software rasterizers rather than about "software rendering" itself.
This could have been corrected on the art side, by recalibrating the texture maps to the voodoo gamma levels, and that’s why there are great arcade machines from that era with wonderful graphics (designed for the hardware they were running in production), but GLQuake looks all washed out.
DF Retro has good comparison of software Quake, GLQuake and VQuake (for the Rendition Verite).
(It even had graphic errors, green textures in the faces etc giving everything a very alien look. But that's not what I mean).