Do you mean this
article? IIRC, this search will be done at the start of the flight rather than after (it's a secondary search before boarding the plane). I've experienced the secondary check when flying from Mexico to NYC (JFK) and it was done by TSA/US Customs.
Additionally, just because they are domestic doesn't mean that they aren't terrorists. There are many home grown terrorists (McVeigh comes to mind). That said, I travel lots. Even with a full beard and F as a gender marker (gender markers are required now as part of passenger info), I've yet to be challenged. I carry a letter from my doctor indicating my trans nature.