Reviving this thread again, curious if anyone has used John's suggestion of the separate lines in Section A and how this may impact the QM points & fees results:
I haven't seen this done, but I wonder whether you could use two lines in section A. On the first line, show the "rate lock fee" in the Borrower Paid before closing column. Then, on another line in Section A (in alphabetic order with the other entries in the section) show "Refund of Rate Lock Fee" and put the amount of the fee as a negative number in the Borrower-Paid at closing column and as a positive number in the Paid by Other (L) column on the same line.