Well, considering that the Gelmorrans had to dwell underneath the Black Shroud because the elementals refused them to live in the forest on the surface, it's highly likely the limit of the 'greenwrath' does not encompass everythign above and below the forest, just everything on the surface within it - naturally if the Garlean fleet flew through the forest instead of over it, it would have been a different story, but from several thousand fulms above the treetops, it's natural the elementals didn't bat an eyelid when Gaius and the Agrius cruised above with their date with Midgardsormr and the Dravanian Horde.

Of course the Garleans later did storm the Black Shroud, raiding Moonspore Grove in an act of genocide against the sylphs (which ultimately just pushed them over the edge into summoning Ramuh and causing the sylvan schism) and then establishing Castrum Oriens in the East Shroud, but that's another story...