After a while you learn to kill mobs to gain more time back on the clock and how to go about that in trying to manage the timer. Than you can work on taking down the Architect in chunks of need be. I've had times where there was over 20 sec remaining on the timer after it was all cleared so I just used a poral to leave instead of waiting around.

Some times I'll clear a little bit of one way towards the one I don't want kill then I'll move and clear out going to the one I want. Depends a lot on the loadout of the room you are in as well. Some times its just bad and you are not going get anything done.