2 and 3 are likely two sides of the same door.
1 is probably a way to reach the vertical tunnel were you end up after the first round with the wheel while controlling the gargoyle.
These are probably just artifacts so the whole map makes sense.
On the other end, there is some hidden room with additional information about the factory.
I'm still not sure if there is an additional secret since the hidden room doesn't mention the sunken city as did the secret rooms from the previous games of the series.