1 - you can't penalize a team because the officials made a mistake. The rule covers this - look it up in the casebook, maybe it's covered there (granting TO when none are available).
2 - The rule says nothing about breaking the huddle with 12. It states that it is a violation for a replaced player to not leave immediately (NF, about 3-5 seconds).
Tell your WH that if he wants to make up his own rules, he should go create his own league.