I have seen some NOS panels that fit horribly, as well, and it wasn't because the body had twisted with age.
Keep in mind that while the $80M press line was used while the cars were in production, once they go out of production that's frequently not the case. Many of the "NOS" quarter panels out there are service replacements that could have been stamped many years after the vehicle went out of production. Once out of production, service panels were typically stamped in a different facility and on different presses than they were when the car was in production (the production presses are too busy making parts for current models). Most of the original dies would have been used, but because the presses are changing over dies frequently to make small runs of service panels, there will be much more variability in the parts coming out. Plus I'm sure die maintenance suffered. Check fixtures and gauges are normally much simpler for service parts, and there's no incoming QC inspector at an assembly plant for the stampers to worry about catching bad panels. The parts were put in boxes and shipped to service warehouses. The first people to see them were body shops... and if the fit wasn't great they just dealt with it.
But... if you can get "NOS", in most cases the fits will still be better than the repro stuff.