I agree the possession wasn't good in that they couldn't get a first down, which isn't entirely surprising being backed up against the goal line, but I think you are mistaken on the timeout. When the Broncos took their timeout, it was after SD had already taken one, so the clock was stopped. The only thing it did was burn one of the Broncos three time outs, which in theory if SD had scored quickly after the punt, the Broncos might have needed to try and match the score.
Anyway, it didn't take 22 seconds off the clock, because the clock was already stopped by the SD time out.