Just returned from my trip to the dealer and 3rd party body shop. I'm a bit more optimistic and a little
less concerned about the extent of the repairs, not quite out of the water yet though.
Click images for larger views.
This first picture shows the different layers of the roof and cross-member that is welded to it, this is what's rubbing together and squeaking;
This picture here shows the spot welds that could potentially be the culprit;
The manager of the body shop is someone who I've worked with before, and said this was an issue they'd have to "kind of throw things at the wall and see what stuck." I let him and the service manager (more-so the service manager) know that I understand they're caught in the middle of this whole ordeal, but if this turns into a situation where I'm without the car for extended periods of time, numerous times, that this issue would become a lot more complex. I think we're all on the same page.
The body shop owner is going to write up an estimate and get it to the service manager, who told me I should expect to hear from him mid next week because the documents and information have to be put through their appropriate processes.