When I was restoring my '55 Ford Courier sedan delivery wagon, I had to cut off the outer rockers, inner rockers and outer rear quarters and some of the underfloor braces at the ends near the inner rockers.
This was all done AFTER I had the whole body sent to a dunk tank where all old paint and rust was chemically removed.
When I got the new panels (some i made on my own), I fitted each panel, then I shot the backside of each one with weld-thru primer and after that was dry, I shot the underside with the overcoat that was to be used as the base coat of the body (aquatone blue, the original color of this car).
I welded all the panels on and prepared the exterior for primer. That was around 1998. The car has sat outside about half of that time and has been used in normal everyday driving including rain, snow, hail, you name it. None of those panels are even beginning to show any sign of rust.
For the most part, these cars rust from inside out.
You may notice that the factory put a large rubber hole plug in the front access to the rocker panels on both sides for Ziebart tar spray application to help prevent rust, but the coating can loosen up and fall off after several years under certain climates.