I know this isn't a perfect solution for when you have unplanned interruptions (postman at the door or something) but between each act of the game you have unlimited* time before aliens spawn. Also, you can cut doors without it affecting this.
So before kicking off the first hive (and like I said, you can do the two doors in the first section) you can wait as long as you want*. After the tentacle and dealing with the door in the corridor (Rhino bit if co-op, seeder/phantom if solo) you can search all you want, open the two doors and take as much time as you want* on a toilet break or whatever just so long as you don't do a hive. The same for the sections on the upper deck and the lab area..
* I've only tested this by leaving it for about 3 hours.. so I think I'm safe putting "unlimited" time