4QXII-a places Jonah after Malachi, so the order of the Twelve wasn’t fixed at Qumran.

Correct, and it is the same pattern seen in Psalms: the individual books are stable while the arrangement of the collection was still settling. The Qumran and Murabba’at copies attest the Twelve with the Masoretic content, and the Greek Nahal Hever scroll shows the same text being carefully revised toward the Hebrew in the first century. Order of books and wording of books are different questions, and only the second bears on the claim.