(q)(2) is not aimed at FFLs.
The behavior you describe
He informed me that they have to secure any purchased firearm in a locked container and walk the customer to their car. I asked him if he was sure it was Federal law and not a BATFE regulation, and he reiterated it was Federal law.
is entirely consistent with the requirements of GFSZ for folks without a license to carry.
You don't mention your state, but I can tell it isn't California (for which you should thank your lucky stars). Here, it is effectively impossible to to open an FFL within 1000 feet of a school. But if one were to exist, locked-case transport would be required to bring firearms to and from that FFL.