Reference edition has nVidia stock cooler, is available earlier than the non-reference....the rest is the same
The fan is not better and not worse, it works differently and has pros and cons. Yes, it cools the GPU less good but it does not raise the internal case temperature as high as usual custom coolers.
If you have a small case or a case with not that good air circulation, the reference is better than the custom ones.
If you have a good case, the custom ones are better.