Hello,
From what I found on a French site the quest start indeed just after the end of "Never Far from the Queen". When I was doing this quest, Aloth was on a mission from the fortress.
So I suppose that now it is impossible to start the Aloth quest? I tried to return to the sewer system or to the sanatorium but nothing happens.
http://www.supersoluce.com/soluce/pillars-eternity/aloth-double-face
Thank you.