The trouble with warp is that it isn't always handled the same way in the movies and the series. There is a DS9 episode where Kira or Dax is very upset about using warp inside a star system, while Kirk uses it without a second thought in STIV, and of course, the Phoenix has no trouble with warping very close to Earth in ST:FC.
I guess that a ship travelling at warp could be compared to a plane flying : the better is in a clear sky, but it's also possible for a plane to fly very close to the ground or in a stormy cloud, but it's a lot more hazardous.
In such a case, it would be possible to warp almost anywhere, but the flight would be much more erratic, less controlled and more dangerous to the ship.
I also usually consider warp more as the ship partially immersing itself into subspace in order to reach speeds not allowed by normal space standard physics (warp 10 would be the ship completely entering subspace, while a transwarp conduit would be a sort of mixed space/subspace wormhole inside subspace). Therefore, a ship going to warp inside an atmosphere would probably cause a lot of turbulences, as some gases are sucked into subspace and where the ship has left normal space, but nothing drastic would happen to the atmosphere as a whole.
Of course, any atmospheric ship flying by would be seriously buffeted around or worse, while a very big ship (like a Borg Cube) warping in atmosphere would probably cause something similar to a tornado.
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Terry Pratchett