I found an answer here [1], via a Reddit thread [2] (where the answers are apparently gone):

    I won't go into details, but if the conductor wants to exit
    the train and leave the doors open at the terminal, he needs 
    to walk to the next car at the last stop in order to open
    the doors, which is why there's a short delay before they
    open. If the doors open immediately at the last stop, then
    it means the train is either going to go to the yard, or the
    crew is going to manually key open one door per car (which
    is only done if the train is going to sit there for at least
    10 minutes, and helps the air comfort system).

[1] http://www.ibtimes.com/mta-worker-goes-underground-share-sub...

[2] https://www.reddit.com/r/IAmA/comments/kx5fa/iama_new_york_c...