Ignore the request. It's a generic e-mail that goes out to everyone. It assumes you don't have a pending new score, because most people with a pending new score don't submit the primary until they have it.
Would you rather risk annoying them by holding your secondary more than 15 days, or risk throwing away several thousand dollars by submitting where your score indicates you are not competitive? If you have FAP, feel free to submit to your heart's content, since you are already an applicant by virtue of submitting the primary and it won't be costing you any money. Otherwise, do yourself a favor and wait until you have your new score.
Yes, all AMCAS schools automatically receive all MCAT scores as soon as they are released. And, no, you will not risk missing any deadlines by waiting for your scores. Whether or not anyone is requesting a 15 day turnaround, all schools prominently list their deadlines on their secondaries. None of them are before mid-October, and many of them extend to December and even beyond.