Originally Posted by Zorak

I'm pretty sure "Upgrade Not Eligible" refers to comp upgrades only and doesn't rule out mileage or certificate supported upgrades. Have you/he tried calling in and asking about it? The relevant thing here is called a Mileage Upgrade Award: Delta Mileage Upgrade Awards

which used to be possible system-wide but are now only available on international flights and a lot of agents might not know about them (and may think you are asking about using miles to pay the cash buy-up offer, which is also a thing), so prepare for a confusing conversation :-/