Your body shop is 100% correct.
The Pantera's roof has no "beams" or "cross-braces" in it. It’s just a large flat piece of tin. In the case of the Pantera all of the "folding" and "twisting" forces within the structure of the uni-body which are commonly transmitted from A-Pillar to C-Pillar through the roof structure, are transmitted via the “roof seam” (or “rain gutter”) around the roofline where the roof pan attaches to the window and door frame. The roof seam is actually an important structural member of the car. It’s like an "I-Beam". If the folding and twisting forces were transmitted via the flat roof panel, the roof panel would twist and fold as it’s flat surface offers no structural strength; it would "oil can" if you understand the term.
Removal of the roof seam would weaken the roof, which in turn would weaken the entire chassis. The roof seam can be removed, but it needs to be removed by somebody who understands what they are removing, and knows what other type of reinforcement to install in its place. This is not the job for a common body shop, but a shop that does custom body work.
The roof seam is OK at transmitting folding forces, but not as efficient at resisting twisting, which contributes to the Pantera's problem with twisting in the rear engine compartment structure.