I can be a bit dense, but I'm not seeing an answer, yet. Inside the last 2 minutes of a half, if the team AHEAD in score commits a foul, the offended team may elect to start the clock on the RFP signal, or the snap. In this case, it wasn't the team ahead in score, so normal rules apply. The clock would start on the RFP signal (no option).
Regarding the 10-second subtraction, that applies (at the option of the offended team) to fouls in the last one minute of the half that CAUSE the clock to stop, like false starts, illegal incomplete passes, etc. A holding foul does not qualify, unless you judge that it was deliberately committed to stop the clock. I suppose it could happen, but it would have to scream "LOOK AT ME - I'M HOLDING THIS GUY ON PURPOSE TO STOP THE CLOCK (EVEN THOUGH OUR RUNNING BACK IS ADVANCING FOR A TD)." Really?
So, in the scenario offered, the clocks simply obey standard clock rules.
Robert