As I read it, the clocks are synchronized using GPS. Just having them identical doesn't account for time dilation if they are at different altitudes (i.e., different levels of gravitational potential), which I believe they are. There has to be some mechanism for correcting their rates to a common standard of simultaneity. That's what the GPS part is for (and it looks like it requires pretty hefty GPS equipment to get that kind of accuracy for the corrections).
Also, I see very precise measurements of distance, but they are all based on GPS location fixes, as far as I can tell. I see a reference to a "common analysis in the ETRF2000 reference frame", but there are no details, just a pointer to a reference at the end of the paper that isn't online. So I can't see if the reference frame they used for their computation of the distance, based on all the measurements, took into account that distance, as well as time, gets distorted when the altitude (i.e., gravitational potential) changes. I would think it would, since they talk about a geodetic survey, which is all about accurate measurements of equipotential surfaces. But it would be nice to have more details.