Honestly, I could buy the fact that a small group of adventurers could outrun a large army on the march and may have a bit of a "calm before the storm" time to try to prepare.
But how in the hells did the giant brain make it to the city, and somehow manage to hide itself underground, all before we got there and without anyone noticing?
Regarding some kind of "major engagement," if one were added, I think it would make sense for it to be that the heroes + allies destroy some sort of bridge or mountain pass, forcing the Absolute's army to take a longer route while the heroes rush ahead.
This wasn't really a major issue for me, but it was just a little bit hard to figure out what the timeline was.
You should go back to the Act 2 meeting of the 3 chosen. They use the netherstones to teleport the brain from its lair under Moonrise towers to the area of the morphic pool behind Bhaal's temple under Baldur's gate city.
Then when you fail to control it with the netherstones and retreat to the astral prism, it rises out of the underground and begins the grand design, calling on the absolutist army , transforming injected to mindflayers and opening the ways for the nautiloids
The story may not be 100% satisfactory (understatement), but you witness the transport of the brain from Moonrise to Baldur's gate when the you see the 3 for the first time and they call upon their stones in Act 2's endgame.
