I haven't read the article yet. However, the ground stations are deeper in the Earth's gravity well than the satellites. That is equivalent to acceleration in relativity.
it is compare to zero gravitation far from Earth. The effect i'm talking about is integral of gravitational dilation change along the path of neutrinos. This path is a chord under Earth surface - the 350 km down to 10km depth and the next 350km bringing back to surface. The dilation change is about 1e-16 per meter of depth.