Not necessarily. Remember, it's a discretionary judgement being made as to whether the shares can be "reasonably expected" to clear before settlement.
I don't think it's hard to think an MM might err on the safe side and mark the trade short. In fact, considering we're primarily discussing OTC issues, it might be the default.
You can lead a horse to water. But you can't make him get down on one knee and do an Al Jolson impression!