The two main issues that GLQuake has over software one are that the textures are squashed down to the nearest power-of-two and lightmaps are clamped in the "0..

The two main issues that GLQuake has over software one are that the textures are squashed down to the nearest power-of-two and lightmaps are clamped in the "0..100%" range whereas the software rasterizer has a (sort of) "0..200%" range. You can see this in the comparisons in the site where bright areas are dulled. Modern source ports have fixed both issues though (FWIW i recommend Quakespasm)