Hi Matt. Not likely any warpage from the TI3 mods - yet. Give us some time.
The crossbrace ball is the only attachment point nearby and can't effect that recessed area of the mold. The Aka Mounts/tube have steel backing plates and actually add overall rigidity to the rear gunwales.
I was looking at all our photos this year, (before the mods as well) and while it's clear that the tubes angle inward, I can also see now that the starboard tube is deflected more than the other.
There's probably variations in tube angles from boat to boat. Wouldn't surprise me if it's a remnant of the cooling process. This was one of the early TI hulls, BTW.
I'll try to get some shots inside the hull soon. Meanwhile, maybe other TI owners can chirp in.
Preferably, by design, these holders would be flared as "outies" rather than "innies". In our case, even storing 2 average poles presents an issue. The pole extenders, which I love, make the problem a little worse.
On this trip, our fishing lines remained crossed the whole time we sailed. Fortunately, luck was with us and we didn't have a single strike.