>A conservative estimate of the height difference between clock and experiment contributes a gravitational red shift uncertainty of 7.7 × 10−17.
So, it appears the 4e-15 is not an actual measured value, but a synthetic value based on estimation and measurement.
They're all listed in table I and the 4.2 * 10^-15 just comes from adding them in quadrature.
It's like when you take a caliper and measure the width of an object, you typically neglect the error due to thermal expansion of the caliper since it's hotter/colder than when it was marked with gradations. If you're really anal about uncertainty (like these guys), you'd estimate the effect of this expansion and say "a conservative estimate says this contributes an uncertainty of 0.0003 mm".