Sora no Woto/WMG

Amazing Freaking Grace is more than just a pretty hymn for Helvetians and Romans.
The fact that the Takemicaduchi had a copy of it and it being universal enough that both Romans and Helvetians over-react upon hearing it might point to Amazing Freaking Grace having a powerful historical significance. Take into account the Culture Chop Suey, and you can have an scenario where Humankind united against "Them" and mobilized all over the world to face the enemy globally, using Amazing Freaking Grace as their battle hymn. When the world went to crap, the mobilized armies were stranded on the spot they were last defending and settled down there. Amazing Freaking Grace was for the survivors of this war a symbol of hope and unity in the face of annihilation.

Sora no Woto is the same universe as Spice and Wolf.

 * In the after-series filler episode, Yumina (the nun) tells Kanata in conversation that she (Yumina) is the daughter of a traveling merchant who goes around the countryside in a horse and cart. Mother is mentioned as just being absent.
 * It's possible that other parts of the world may have even regressed further into Medieval-like conditions. So it's not that far-off an idea.

The Time Telling Fortress is Antarctica.

 * The garrison consists of two naive rookies, a royal bastard whose presence is, until story's end, a political embarrassment, and two shell shocked vets. This is the place the military sends people they don't want near anything important. It has enough value to necessitate some military presence, but not enough for a substantial one (since I doubt anyone contemplated an attack over No Man's Land). So they send soldiers who would be liabilities in normal circumstances, but for some reason are important enough that they can't dismiss entirely, to the place.

The Sora no Woto world is actually the future of Battle: Los Angeles.

 * The humans put up a valiant fight, and eventually develop their own advanced weaponry to fight the aliens, but they ultimately lose and are forced to retreat into the small pocket of land the current nations are located in. The aliens eventually leave after they've drained the majority of Earth's water, which is what caused most of the planet to become No Man's Land.

Angels destroying the world?

 * Where have I heard that before?

"Them" were Bird Men.

 * Think of Sora no Woto as an alternative follow-up to Macross Zero where the Bird Man came back with friends to annihilate Mankind. Too bad there isn't a Love Triangle...

The world is a prequel to the world we see in Nausicaa of the Valley Of the Winds.

 * The world is devastated and poisoned. No fish in the sea, it's becoming sand, and the little pocket kingdom of Seize has a very similar feel to Nausicaa's home. It also could be that the "Them" that destroyed the world are the biological monstrosities found in Nausicaa, and were distorted yet again in legend into being something they weren't.