Ford did the same damn thing to 2 out of my 3 Tbirds! I was sent a letter from the stealership regarding a free inspection they were offering (for cars purchased from there), so I ate the bait and let them inspect it, and they DID use a floor jack for the first part of the inspection too.
My pinch weld was folded over in some spots, but the area that is dented upward near the body plug like in your pics is what really pissed me off!! I lifted up the carpet and padding on my Tbird as shown in the pic (got the car in 1997 in High School), and went at it with a hammer and got it straightened out most of the way since that car I wanted to be as close to perfect as possible, and took that car regularly to shows/meets, drag strip, etc..
I was never able to get Santa Monica Ford to admit to it, on both of my MN12's... You would think with how much the stealership gouges on the prices, that they would at least care for these cars much better than a Pep Boys or Midas would! I handled all the maintenance, repairs and mods on my cars ever since!
I bought my Mark VIII like this though - pinch welds on both sides, all dented up and folded over... in fact, on the drivers side towards the front of the car, the pinch weld faces outward now, and towards the back on the same side its folded inward!
On my Mark though, I think its a combination of having some jack-asses working on the car, along with the previous owner's wonderful driving skills!
FYI - the pic was taken after rebuilding literally everything on my suspension with polyurethane bushings, new sway-bars with custom end links, 97 front and rear spindles and cobra brakes, rear disc conversion, and tons of other goodies... I had temporarily put the car back together with Monroe sensatrac shocks, and stock springs to run it for a month or two (which is why it was sitting so high up) before throwing Koni's on with H&R springs. A little off subject, but I know someone is gonna tell me my car looks strange so I thought I would explain...