This part also made me think of Corypheus' line “Beg that I succeed, for I have seen the throne of the gods, and it was empty.”
This empty throne could thus fall in with the Black City/Golden City theories that have gone around.
But there is definitely more to Skyhold. I wonder if we'll find it out.
Well, Inquisitor's throne is also vacant, because he/she is in the Fade atm 
Besides - I highly suspect that something that is supposed to be the seat of the Maker (or at least for someone with great power) the interaction with which unleashed the Blight on the world, it would be something far more imposing and not just a more-or-less random prop found only if we search the area.
A lot of deal is also made of unlocking gates to the Golden/Black city, with Morrigan hinting that the Anchor and therefore Inquisitor being able to potentially do this - and I don't think they'd be actively trying to make that plot point irrelevant, or make the whole 'entering of the Black City' anti-climactic.... because it WOULD make the whole thing seem as not as big of a deal - I mean, it IS a big deal that Kieran/Flemeth were able to re-direct eluvian to the Fade, but even with all the things happening, is nobody really noticing that they're supposed to be in the location widely considered to be either center of enormous power or center of the Fade??
You'd think the Black city would make a far bigger impression on IQ and the rest - plus, it would likely have its consequences (again, the previous visit unleashed the Blight on the world and turned magisters into darkspawn).
I mean, even Solas seems to be determined to reach the Black City - after all, one of his first remarks about the Fade is "look, the Black City, almost close enough to touch". This, among other things, is making it rather obvious that IF we're going to enter it (be wit with IQ or any other PC in future game) it's likely going to be a HUGE deal.