The irony is that the new rules were meant to reduce the burden on foreign GA operators to seek waivers from the TSA when flying to, from, or between US airports.
The new rules were supposed to exempt GA flights below a threshold MTOW from needing TSA approval.
But it seems an error was made in drafting the language of the new rules with regards to overflights from previously exempt countries.
From what I heard TSA began to correct the mistake immediately and issued blanket exemptions to operators within hours.