In the caption under the image it explains that the 3Dfx card lacked gamma correction, which is why it looked so saturated. The Voodoo was a pass-through card: it had its own DAC for generating display signal when a full screen 3D game was running, but otherwise your 2D accelerator was used. So on the same machine a software rendered game and a 3D accelerated game had different output even if the frame buffer was identical, due to different circuitry (and the Voodoo card’s circuitry lacking gamma correction made it hella saturated as you see here).

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.