I think the physical side of whatever the Black City is, exists at the center of the planet. Which is why it can be seen from everywhere in the Fade. (I don't think it's Arlathan though.) And after the magisters unlocked it like Pandora's Box, they came out of there tainted, unleashing the Blight along with them. That's why they emerged from underground. I wonder though if the Blight is something intrinsic to Thedas' cosmology, or if it was created. If it was created, the main suspects are the elves and the dwarves. I don't know if the elves created it, because it sounds like it's something they mostly avoided unless we're talking about Andruil, and it sounds like she used it as a playground rather than created it. There's some evidence from the primeval thaig that ancient dwarves may have worshipped it (possibly the Stone?), but that might suggest they didn't create it either. What all this does tell us is that the Blight predates the Tevinter Imperium, which means the magisters didn't create it, only released it. While the elves may not have created it, it's possible they weaponized it, and it may even have been the rumored weapon Fen'Harel promised each side of the elven pantheon before sealing them away.
Another possibility I've wondered about, is if the Forgotten Ones were the leaders of elves living even deeper underground than the dwarves with the help of magic (such as the eluvians). Maybe the Black City belonged to them, and they created and *controlled* the Blight long ago. And that's why the Old Gods still hold sway over the darkspawn.
Tell that to the people who had to pick between Hawke and Alistair.
*sobbing forever* My Surana and Zevran are my last happy couple... *protects them fiercely*