As far as I understand space comms--which isn't that far--the 'pilot beam' technique used by satellite links is more or less a way to get a phase lock on the signal beam, which will accurately determine the exact target location, at which point the space transmitter can use a beam-forming antenna to to jack up the power to that locale specifically, giving better SNR/bandwidth/whatever. The key bit here is that (a) the method requires that the target--i.e. your bedroom window--transmits the pilot beam up, and (b) only 'solves' the atmospheric interference issue by pointing a powerful beam accurately.
Don't get me wrong, it could probably be done with enough money, and if anybody could do it would would be the US intelligence machine. Same goes for a drone, to a lesser extent. With anything flying in the atmosphere you'll have to do deal with local vibrations on the same order as the measurement deltas you care about, but there are ways to do that too. It's interesting, thinking about it now, that a lot of what we're developing could actually be directly applied to such an endeavor, even though we're not related to such industries at all. Fun.