As you are championing Alternative 1, the NPRM already contains the
FAA's reason for not adopting it:

[...] The FAA believes that the threat
of terrorists using aircraft as missiles
must be guarded against, and this option
would not adequately achieve that goal.

Conclusion: Rescinding these actions
would increase the vulnerability and
diminish the level of protection...

Well, either they have already made their decision (and further noise is
unnecessary even in what we considered a free state) or these are the
points that need to be rebutted. Alas, without actual data (which is
certainly classified) this will be difficult, as the response is
guaranteed to be "petitioner is wrong because of {CLASSIFIED}."

The NPRM contains the reasons for the decision that has already been
made. Our only hope is that the decision hasn't actually already been made.

Jose
--
Quantum Mechanics is like this: God =does= play dice with the universe,
except there's no God, and there's no dice. And maybe there's no universe.
for Email, make the obvious change in the address.