It can't compensate for the effect in the linked-to article (namely, the fact that the distance and flight time between the neutrino source and destination is shorter according to the satellite, versus an observer on the ground) because that effect depends on the specifics of the experiment.
Consider this: If you flipped the location of the neutrino source and destination, you'd actually get the reverse effect (neutrinos would appear to be going slower than light).
So it's up to observers on the ground to compensate for relativistic effects of this nature.
(As I mentioned in another comment, I would be shocked if they didn't already do that)