I think we can headcanon whatever we want but ultimately the Skyhold is no longer the full home of our Inquisitor and is no longer the full headquarters of the Inquistion as we knew it from Post-Skyhold until Trespasser.
We can imagine what we want, just as we could imagine much of the several year gap for the Warden-Commander, and couple year gap for Hawke (and gaps between the Acts in DA2).
In any case, the place won't be a big deal for now. This doesn't mean its done forever. Like I gave the example of its use in a Dragon Age MMO. Or it could be revisited in a future SP game.
The gist is that we've only seen the top layer and a big of the layer under it. For all we know, there's even more to Skyhold and it'll be uncovered and important later.
I wish that wasn't the case but eh.