Yeah, I was also confused on the timing of the Underdark events.
Not sure if they've changed dialogue, etc. But Halsin used to, at least, say that Ketheric built the Grymforge stronghold in preparation for using it as his main base of operations because it was accessible to both Moonrise Towers and the Temple. However, Halsin and company defeated him at Grymforge before he could properly launch an assault from there.
So, again, things don't add up.
I had a post about this stuff before, mentioning the inconsistencies of the story and how confusing it was. That's when I first brought up the Halsin-Aradin they've been gone over a month and a half but the temple's 5 minutes away thing. Stuff like that makes no sense and lends to the theory that Larian staff are not all on the same page. We need continuity and clarity.
I love a good mystery, but a good mystery REQUIRES continuity. Throw off even 1 detail, and the whole mystery is blown.
It seems to me that some of the problems are EA's fault.
Considering that some things have changed quite drastically (if you haven't been following datamining you have to take my word for it), it is likely that at the beginning of EA they weren't quite sure about certain things. According to Swen, the project itself got quite big, which probably also forced some changes.
I wouldn't expect all the story holes to be removed, but I suspect that some of the story will be sorted out in the full version.
At the moment, it's hard to say what is up-to-date and what is not.
