Kale, it is just another way to look at clock management. Rather than "why the clock stopped," look at what ultimately happened after the clock stopped, and what the rules say about starting the clock.
In "a", the clock will start on the ready for play, because 3-2-3-e-4 says to start the clock on the R's signal following completion of a penalty. Yes, there is an exception that allows the offended team to elect to have the clock started on the snap, with less than 2 minutes in the 2nd or 4th periods. But the basic rule is that the clock starts on the ready after completing a penalty (and there is no other superseding reason to start it on the snap).
In "b", there is still no superseding reason to start the clock on the snap, so 3-2-3-e-4 still governs, and the clock starts on the ready.
But, let's say A scores an apparent TD on the play. Completion of the penalty and the apparent score both stop the clock. But, the apparent score supersedes the completion of the penalty, with respect to starting the clock, so the clock would start on the snap.
Or, the BC goes OB. The clock stopped both for the OB and to complete the penalty, but the rules governing when the clock starts take over. If inside 2 mins in the half, the clock starts on the snap, which would also supersede completion of the penalty, and it starts on the snap.
In your AR example, the clock stopped both for the OB and to complete the penalty, but the rules governing when the clock starts take over.
As a Referee, I don't care what stopped the clock. I only care about when, by rule, I am to start the clock. There may be multiple apparent reasons to stop the clock, but ultimately, there is a single governing reason to start the clock.