Even if the custodian writes the check directly to the charity, the instructions for form 1099-R still tell them to put the entire distribution in box 2a and check the "taxable amount not determined" box. The only time they wouldn't check that box for an IRA is if the entire amount in box 1 is a direct rollover to a qualified plan or another tIRA.
This is because an IRA custodian has no way of knowing whether or not you have other IRA accounts and what you did with them. They can't just assume a gift to charity is a QCD even if they send the check themselves. You could give $105K from one IRA and $50K from another, but you can only exclude $105K from income, so there would be a problem if you had two 1099-Rs and they both had $0 in box 2a.
This is because an IRA custodian has no way of knowing whether or not you have other IRA accounts and what you did with them. They can't just assume a gift to charity is a QCD even if they send the check themselves. You could give $105K from one IRA and $50K from another, but you can only exclude $105K from income, so there would be a problem if you had two 1099-Rs and they both had $0 in box 2a.