I can't find this scenario in the instructions but I assume it is describing allowing a rollover of an RMD and not the second part; effectively correcting it by making a later distribution.
I agree that without the later deposit, this is fixed by issuing 2 1099-Rs and the participant could/should withdraw that as an excess contribution. But I also think that the way it was handled was fine; frankly, the IRS doesn't care that much about which distribution was the RMD as long as it was done. I also think this guy may be surprised and unhappy if you follow the rules - it sounds like he wants a 1099-R showing 100% rolled over, and that would definitely not be correct. If he has the money and is willing to write a check to the plan but not to the IRA he's just being a jerk and asking for trouble since the 1099-Rs will be spanning two years, and while we might all be surprised at what the IRS does not look at, I'm pretty sure they are matching 1099-Rs to what is reported on the 1040.
Further, if he took the RMD from the IRA as he claims, he probably did it as a regular distribution and not an excess, and (again) if the plan processes the 1099-Rs correctly, he's done the wrong thing and should at the very least get that code changed to an excess, not regular distribution.
Long story short, it sounds like he wants the plan to report based on what he did, not what is correct. The plan has no way to know that he took the RMD and must report accurately.