I imagine that over the years, normal reality will slowly overgrow Sotha Sil's Clockwork City again and ever so slowly undo his project of reshaping the world from within.

Another interesting thing to note is the words " My city is where I live, and I live in my city. Its location is unimportant, as I am its only citizen." Curiously, the only physical way out of the city seems to have collapsed (in an otherwise pristine mechanical environment) the moment that Seht passed away.

I've always said the Clockwork City is a solispsitic fabrication that only exists in his mind. But no one ever really went with it.

Surely it would have been relatively simple to script them so they didn't attack after you complete tribunal?

Well I have thought about the sentence "My city is where I live, and I live in my city. Its location is unimportant, as I am its only citizen." But I dont feel as that would be it as you were actually there, atleast in a part of the city.

But then again, the last "entrance" to the city may have been destroyed.

That was only the entrance to his workshop, according to Fyr. There may be a larger entrance to the main city.

What happened to the Battlespire? Without it's master or protector, may the Clockwork City befall a similar fate?

I don't know where the City is, but I've always thought it's in some "pocket realm" like the Battlespire... As in, somewhere in Oblivion.