Well, this part of the article suggests they ARE comparing it to the speed of light in the medium:
“Light would have covered the distance in around 2.4 thousandths of a second, but the neutrinos took 60 nanoseconds - or 60 billionths of a second - less than light beams would have taken.”
Might just be a poorly written article though.
No, they're just talking about the distance divided by C. This wasn't a race between photons and neutrinos. It's just a matter of how fast the neutrinos were moving.
BTW, I suspect a measurement problem somewhere rather than a violation of relativity. But it would certainly be interesting if this turned out to be real.