The custodian can only know that the distribution was paid directly to an entity other than the individual for whom the account is maintained. The custodian cannot know that this actually qualifies as a QCD because the custodian has no way to know (or at least is not required to know) if the entity to which the payment was sent is a qualified charity, has no way to know the actual amount that would otherwise be taxable and has no way to know if when combined with such distributions from other custodians that the total does not exceed the annual $100k limit for QCDs. Since the custodian cannot know how much, if any, of the distribution qualifies as a QCD, it's impractical to indicate a QCD on Form 1099-R.
