The real neat trick is time transfer from device to device and handling the bookkeeping appropriately as one transfers time from stationary devices to moving devices such as aircraft.
Not just moving devices - altitude too, so your aircraft was a good example. Time passes more slowly the closer you are to a centre of gravity. There was a TV programme a couple of years ago where they synchronised two portable atomic clocks, then took one up to the top of Snowdon and back. That one was then found to be ahead of the other because it had run faster when at altitude.
So if you really need the precision of atomic clocks, then you are going to have to allow for altitude.