I've seen it a few handful of times when someone is registering after the POT deadline occurs, but has a valid POT from within the calendar window. What I would do is get into the race, and then upon confirmation send runDisney an email stating you just registered and didn't properly submit the POT and since it's past the deadline you can't fix it on your end. Low chance they might help you, but worth a shot. And then as you said, go to the runner relations and see if they'll help. In most cases, they'll fix the error if it was on their end, but on rare occasion when the error was yours they will fix it. Bring the evidence, a smile, and a positive mindset. I wouldn't say it's impossible, but register knowing that the chances are low that he'll get into Corral A.
If he started in the first non-POT corral, it'll probably be like 14 min after the gun time. If he aims to run around his PR pace (7:10 min/mile), then he's about 4 min/mile faster than those starting with him, and about 2 min/mile than those who started 10 min before him. So if he stays patient, starts near the front of Corral D, then he'll find the course opens up a good bit upon entering the highway around Mile 1.5-2. By the time he gets to TTC (Mile 4), he will have passed most of the runners that started ahead of him in Corral B-D, and be catching those in the backend of Corral A running their PR pace (if they are). So my suggestion is not to stress too much about the opening 2 miles until you hit those wide highways and then he'll find more space to move. But it's unlikely he'll be congested by the time he makes it to MK given his pace.