As supported by the official guidance below, if a loan exceeds the QM 3% in points and fees, the lender can always issue a lender credit to bring the loan into compliance before closing:
iv. Creditor-paid charges. Charges that are paid by the creditor, other than loan originator compensation paid by the creditor that is required to be included in points and fees under § 1026.32(b)(1)(ii), are excluded from points and fees. [Official Interpretations]