Yes, but as far as the argument in the paper goes, A's velocity doesn't even matter, all that matters is the time on the satellite clock when the neutrino was emitted from A, the distance between the stations, and the velocity of B relative to the satellite. The difference in latitude would change the exact result somewhat because the neutrino is not travelling exactly along the velocity, but to be fair, I'm pretty sure the author mentioned that this was not an exact calculation, just a suggestion of where to look for an error.