Good question. There are actually many reasons. The 991 Cup car was available some time before the road GT3 so when the Cup was launched the 9A1 derivative wasn't even available. The old engine remains homologated for a number of years, and most believe that there will be substantial changes to the Cup circuit specifications within the next year so really it is common sense for them not to switch the racing cars over immediately.
Among other things, the GT3 is an incredible value. As far as "the best 911 ever"….I think that beauty is in the eye of the beholder. A friend of mine owns an RS 4.0 (997) , that I have driven a number of times and that car (manual) provides a driving experience that is truly memorable. I can't wait to see the RS and H.O. versions of the new GT3 when they come out.