Under NCAA rules, we don't have a dead ball foul for simple offsides, so we'll just assume it was offsides with contact, causing a dead ball foul and stopped clock at 6 like the OP said.
First, no time is put on the clock. 2 seconds is reasonable in that situation. We mark off 5 yards, then I tell both teams that the clock will start on the ready. If A does not get the play off, that's on them. As soon as a RFP is blown, we have a new play and its THAT play that is determinative as to whether we extend the period.
Second, defensive foul has nothing to do with whether the period ends. Its a down free from live ball fouls. The down, by definition, starts at the ready for play.
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