Although there's no financial incentive for YC here, the financial cost for the few non-profits they decide to fund is nominal as well. YC has the money to fun

Although there's no financial incentive for YC here, the financial cost for the few non-profits they decide to fund is nominal as well. YC has the money to fund many more companies than they do. But not the bandwidth. Y Combinator is not selling their capital, they're selling their time, expertise, and network. A separate fund would defeat that purpose.