Very good, well framed question, but the only people who could possibly answer it with assurance work for FinCEN. They are not final because they are right, they are right because they are final.
I suggest you start with the Helpline and confirm your conversation in writing, but I would have to assume your vendor already did that before it made the change.
P.S. FWIW, I agree with you. If this was a Joint Report; i.e. multiple banks were filing the same report, but all of the activity was at the branch level, your vendor would be listing each individual branch in its own part III. Note also that items 62 & 63 reference a number and financial amount that apply to the bank as a whole, not to an individual branch.
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In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.