Looks like this thread already covered a lot of possibilities while I've been away from FT, but I think we are discounting the possibility of gate agent/contractor incompetence. I had a similar experience where Turkish Ground (TGS, not Gozen) tried to deny boarding at the gate to my US LPR spouse on an IST-MUC-LHR-YVR itinerary operated by TK/LH/AC on a single ticket number back in the days when you could stitch together more creative award routings with UA miles. The issue for them was that they believed that there was no possible way to do an airside transit from TK to LH at MUC. I knew they were wrong and protested as much as I could while pointing to Timatic Web printouts as the boarding process continued. Sure enough, TGS backed down just before the gate closed and we were on our way.

Anyway, the point is that the gate agents and contractors who work non-TATL flights do not seem to have a good sense of the nuances of the TWOV policies and concessions that facilitate travel for US residents and visitors, and I fear that it is sometimes necessary to be as assertive as one can be with them without causing a scene.