Questions about the last subway trains of the night

Held means held, so if a train is running a bit late(as your train was) all connecting trains will hold. The Mattapan trains will hold for Ashmont trains as long as it takes, regardless of when the train comes.
And no, you aren't charged an exit fare on the bus. Don't know about the zoned charges for those buses(if there are any) but I doubt there would be any or else the schedule would say so.