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The PoA was doing a pretty good job hovering at the end of Reach.
I am gonna go out on a limb and say "rated for atmosphere" means the ship is equipped with something or other which makes it more effective in atmosphere.
The dude in Halo 3 said "Is the Dawn rated for Atmosphere?"
You can surmise that, from this comment, that not all Frigates, or UNSC ships for that matter, are equipped to handle Atmosphere roles. That's why some ships were being built in orbit, and other ships were being built on the ground, as seen during Long Night of Solace and Boneyard respectively.
So any ship class can work in Atmosphere, it just might require some special piece of equipment or engine configuration or something.
But this is just speculation.