Yes unfortunately once your past the 3yr/36K miles bumper to bumper warranty you're on your regarding this issue. Ford is apparently offering no help whatsoever for those whose cars or trucks are out of warranty. Which as a loyal Ford owner since 1984 and former Ford and Lincoln Mercury dealership service dept employee I find outrageous since there is clearly a manufacturing issue with the aluminum hoods. I guess Ford will not do anything unless their hand is forced by the courts as it was by the 3.8 V6 head-gasket debacle in the 1990's. So far as far as I know there has been one unsuccessful lawsuit against Ford over this which I saw on the news, and someone posted here a while ago about starting a class action suit but they never followed up so I have no idea where that went if anywhere.
As far as repairing it, from what I have read here on Stangnet, on other Mustang forums and various Mustang FB pages the problem often returns after stripping, sanding and respraying the hood. It seems that the only way to be 100% certain that it will not return is to go with an aftermarket fiberglass hood.Ford did put out a TSB for this problem for earlier S197s Mustang hoods. It's It doesn't apply to your year,and it doesn't provide for any additional warranty coverage past 3/36 but it does provide a repair procedure so but maybe having your body shop follow the procedure in the bulletin will work. Good luck!