I always love seeing how you prep for a panel replacement... I like how you modified the rocker as well. I know its a lot of work, but I think you'll be pleased with the result.
6:45 id blame a lot of that on the moisture collection via condensation. the xjs are horrible for it. the coatings are not designed to have moisture on them for days and months at a time like they tend to see. the moisture will eventually pernitrate because of this. its why boats get gelcoat and not paint. once the moisture gets to the metal. all the rest of what you stated comes into play. salt, rocks hitting it, etc. its a bear.
After you got everything welded up get some 3 m cavity way it has a 12 inch hose with a 360 degree sprayer on the end that will coat the inside of the rocker's don't use under coating it will hold moisture and rust I been doing this trade 30 years i've seen it all good luck buddy.