I'm sorry, but unless something has changed in the *very* recent past, that is not true.
DME is transportation from MCO to your WDW resort and back. That's it. There is no requirement to be arriving at MCO on a plane, and there are many situations where someone would be at MCO without having arrived on a flight: Some people are staying a night in a nearby hotel. Some are on a non-Disney cruise and their cruise transfer will only get them back to MCO. And some, like the OP, are dropping their rental car off at the airport because it's cheaper.
In all of those situations, if you call Magical Express directly at 866-599-0951, explain the situation and tell them approximately what time you'll want to take the bus from the airport to your hotel, they'll schedule you into the system without associated flight numbers. They've done so many, many times. In fact, I usually suggest to people that they call DME direct at the above number rather than try to get a Disney CM at the reservations center to try and schedule it since the DME people are used to the out-of-the-ordinary situations.
Since they were calling at 3am Eastern, my guess is that the OP got the overnight person who's on duty primarily to handle immediate same-day issues like delayed planes, cancelled flights, lost luggage, etc.
So, I'd suggest you try calling back during the regular 9am-5pm Eastern Time workday to get someone who isn't the overnight coverage person. Or you can do as others have said, find a flight arriving close to the proper time, give that flight info and be done with it.
-Rob
