So I did get in touch with the admissions team and this is what they said...
"You may submit without that recommendation and still be considered in second round. It creates a LOT of extra work on our part to match individual recommendations, however, so please encourage him to submit it before 5pm tomorrow if at all possible. If he can’t make that deadline, then please just have him submit it as soon as possible afterward – definitely within a day or so."
"We can't guarantee that your application will be read with all three recommendations unless it comes in very soon after the deadline. We'll start reading files on Saturday. In the unlikely event that yours is read on Saturday and your recommendation isn't submitted, then we'll read it with just the two.... That's why it's important to get these things in timely!"
So that's that. And I'll just have to wait and hope it makes it in time.
Quick question on this though - when you opt for the "send a reminder" option on the recommendations page, does the recommender come to know you sent him the alert... or does it appear like an automated alert from the school. I really don't want to pester him with my constant reminders.