Those numbers are averages. Maybe they get a lot of larger donors or recurring donors. It's quite possible that they wasted his entire donation trying to convert him from a $50 donor into a $1000+ donor.
Possibly. But if so, they do that for a simple reason: "Upselling" past donors will in most situations have substantially higher conversion rates than obtaining new donors. It may not have been cost-effective in his specific case, but it's likely a cost-effective use of their resources on average.