From the builds that I have followed where they removed them, the biggest concern (beyond getting good welds) was to not remove the entire gutter at one time. They work a few inches at a time, or trim out sections, weld them up, and them trim out the remaining sections. This keeps the roof skin from popping free of the the lower structure.
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.
The simplest thing, if you're thinking of aerodynamic improvement, is to only remove the section running down the a-pillers. Fold over and/or weld that seam without fear of buckling and leave the structural sections on top, with or without the chrome gutter. Then at Daytona, you'll gain 2-4 mph in top gear.... Works on Porsches, should work for us too.

If its just for appearance and you want it all gone, its a MAJOR alteration. Wilkinson's shop has done at least one of these. Check with him for details & pricing.
FWIW, consider that it's a huge amount of cost and effort, and may have a negative impact on both structure and future resale.

If you're like me, the last part will only impact your estate (who cares...). But unlike so many other positive changes, this one is near impossible to reverse after completed. So be 100% sure before you get the grinder out.

Mark
I am doing this on my current build as well. The way I am tackling it is I create multiple notches in the rail and tack weld at each notch until I feel there are enough to keep the roof sheet tight to the side. After that I will remove anything else and weld. I have a pulser module on my tig that will keep the heat minimal. I do have a roll cage though That will be tabbed in everywhere.
I think key to rigidity will be tying the roll cage into the upper structure somehow, probably a six point cage that ties into the rear decklid hinge pints or double wall roof structure achieves that best.
The roof is going to be stronger with the rain gutter removed if you do it right !
Original the roof is spot welded 1 inch a part if you seam weld it its going to be stronger! but you have to now what you are doing, Weld it good and not grind the weld to much! On rally cars all spot welds are seam welded and it make a very big difference in stiffness. The small strip you cut off has no positive effect on the roof strength to begin with because the bigger part of it is on the outside of the spot welds. I recommend to tig weld it because the weld is tougher than mig weld and it is easier to get a good bonding. And if the car is in an accident the weld will not crack!
The only negative thing with tig welding the roof is heat you have to be very careful.
I've done it, not hard. Easy to get good penetration. Hardest part I had was keeping the line smooth. Small changes in cut off blade or torch placement made a significant difference in the finished smoothness of the mod (ya don't want a wavy seam there)

Like everyone said before, cut a section, weld it till it won't move, then cut the next section. Then come back and weld it up slowly with even heat across the roof.

Go slow, take your time. The roof behaves better than I would have thought regarding heat.

If you've got a cage, gusset it to the a and b pillar and then stich weld it to the roofline.

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