So I was ready to ask a follow up, but I think I managed to answer my own question by finding a different.... quirk.... in the rules.
I was going to ask, "A35 runs for a TD, but A65 holds on the play -- clock starts on the snap because TD, except TD didn't happen due to foul (same as new series (not) being awarded for R after the punt)" -- that's different, but why?
I think I found the answer in 3-4-4 that lists situations where the clock should be stopped. The clock should be stopped due to a score or touchback or when the down ends following a foul -- but "B or R awarded a new series" is not actually listed as a reason why the clock should be stopped. Of course, "if the clock was stopped because ... B or R is awarded a new series" IS listed in 3-4-3 as a reason to start on the snap, but there's no actual rule support that we should have stopped it in the first place?