OK, so let me sum this up:
The Machines' Tabor building has been moved to Akasaka, and stairs have been added to the Bishop Imports tower in the Ueno neighborhood... wait, no, nothing of that has happened, it's just mission characters and controllers talking weird stuff! Brainwashing, maybe?
Kidding aside, I just hope that Gray's text is going to be corrected when this mission pack is released in the upcoming archive. As a reminder, the new Machines mission "Meet with Agent Gray" was said to take place and took place in the McClane Tower in Akasaka, yet he speaks of the "Machine building in Tabor Park".
Also, something I don't understand is the talk about the stairs in the Ueno building. The only stairs there can be accessed from the rooftops of the two towers, and those just lead to the passage to the elevator -- there aren't any doors leading to mission areas or anything. Was that where the stairs stopped? I'm apologizing then.
However, it's still weird: We know this building, we can access it and go inside, and we know there are unaccessible floors where Niobe is located. And yet, this building is just in the same state as always. How story canon is Mega City anyway??