They're trying to be kind to the people they just refused, I'm not sure why that's pretentious. If you applied, presumably you wanted to get in and reminding them that it's not necessarily them or their company which is wrong is a kind thing to do.
Actually, I think this is the most important part of the process. When you're small you have the luxury of making mistakes and no one cares. When you wield some power/prestige and your actions affect other peoples' lives, people start coming to you with grievances. The worst part is that often those grievances are "deserved" --- I guarantee that some startup w/o an interview request will make it big, and one that gets accepted will slink off and die. That doesn't mean that YC is failing, just that the problem is really hard.
The problem itself isn't very hard, at least not in the mathematical sense of the word. It's just that it's a human process, and is thus prone to the failings of human beings, including the various biases that human beings are known to have.
Perhaps being "kind" was the motivation. Maybe it was business oriented though. They are in the business of getting all the choice investment opportunities coming to them. So, it's in their interest to have people not discouraged from reapplying, or to have them bad talking YC because they "Couldn't understand my awesome idea".
