Hi Richard,
One thing that the TSA did not mention in the ruling, is that this only applies to FAR Part 141 Schools. Only FAR Part 141 Schools have Visa Authority to Issue I-20s for Foreign Students to train in the U.S. and this Rule only applies to Foreign Students that are training towards a Certificate, Licence, or Rating.
This isn't how it is being interpreted elsewhere. Today I was at a flight school in another FAA region, and they have been told you need to go through the TSA checks even if you are just checking a foreign pilot out to rent a plane, and also for a BFR. That's Part 61 activity. It seems likely that in due course this will also apply to US citizens. They are getting out of the training business.