My guess is that the escalators are alligned to minimize conflicts with Line 1 crowds so they allign with and prioritize access to the exits to the street
(to minimize common corridors with Line 1 crowds).
The level below the Line 1 Queen platforms could be a transfer level to access Line 1 platforms without conflicting with exitting Line 1 crowds.
I suppose the void area is just a consequence of the depth of the tunnel required to pass below other subsurface structures under Queen St. (PATH passages and utilities). The void area seems to be centred on Yonge St., maybe to minimize construction work near/below the intersection.
Just to add one note here for people.
The level you currently use at Queen St. Station, to get from the SB to the NB side and vice versa, is, in essence the platform level for the Queen Street subway (likely streetcar subway) that was constructed at the same time as the original station, as it was thought at the time that an E-W line was likely to run under Queen.
You may have noted that there are in fact, 2 different passages, one to the north, and one the south.
The void in the middle is where the tunnel and space for the tracks are (there are no tracks)
What you need to realize though is that track level is below platform level.
This image below is from BlogTo:
Credit: BlogTo
You can see the little yellow stair case in the distance, that takes you up to the level you are on when you walk under the Line 1 tracks.
The new line is being built below this.
I take it they need come in a certain minimum distance underneath; and in any event, they probably require significant ceiling clearances under the fire code.
Beyond that I'm not sure why the box is exactly where it is; there will be people here more expert than I on such things.
Just thought I would share that the above is likely a part of the story.