I'm not going to comment on Mr. Rockwell as a source in general, but as a long time FA owner, I can tell you that the FA only applies "last look" corrections in S and P modes and not A nor M modes. So for DOF purposes, Mr. Rockwell's claim is a red herring. If you think about how Nikon's aperture lever works, you'll see this has to be the case. (From language in the manual, I think it only applies such corrections when it can't detect an AI-S or Series E lens, but I'm less sure of that.)
You might be able to get a lens re-engraved with T-stops, but unless you also recalibrated the detents you'd still be shooting in f/stops. Since DOF is a subjective "acceptably sharp" criteria to begin with, I suggest you relax, don't worry, and save your money for outings, film, prints, etc.
Thanks for the clarification and the nice writing!
Fed 2, 4, 5
Zenit 11, 12XP
Olympus OM-1N, OM-2N, OM10, OMG
A bunch of Nikons