The 90 day delay is a way for the system to protect both parties involved, the seller as well as the affiliate.
Delayed payments are a perfect way for the affiliate and seller to create a relationship of trust. The delayed payment option allows a seller to hold the money in case a refund is processed. This process gives sellers confidence to open sales to more affiliates, and it offers affiliates an opportunity to gain the trust of more sellers. Once trust is established the seller can move the affiliate to instant payments. The seller pays the commission after 90 days, or they can pay out prior to that, at their own discretion.