Not to disagree with anyone but...
the root cause is the contact of dissimilar metals - aluminum againsts steel. Heat from the exhaust only accelerates the chemical process, but
does not initiate it. The factory fix was galvanized sheet metal screws because the galvanized coating was a sacrificial material- it corroded instead of the side sill. (Same idea as those anode radiator caps...)
Repainting helps only while the new paint acts as an insulating layer between the aluminum and steel. The permanent fix is permanent insulation between the parts. This sounds goofy, but when I got my sills replaced under warranty in 1999 I put duct tape on the inside where it contacts the strips on the frame. I have used the galvanized Dodge screws and also Home Depot screws that come with a sealing washer - one with a captured rubber gasket under the washer. This way the screw is insulated from the frame.
No, duct tape is not a permanent fix, but since I've changed the exhaust a few times it was (OK, accidentally) replaced several times. Perhaps some header wrap is a longer lasting idea. Nylon washers or high temp silicone might be other options. If anyone has restored an original Cobra (not me!) they have faced the same issue since the aluminum fenders were riveted to the steel frame. Ask a car restoration shop what they would do.
Guess what - for all the abuse my car gets (wash once a year whether it needs it or not, drive in the winter and rain, cats in the exhaust, multiple stone chips and rock hits leaving no paint behind front wheel) there aren't any bubbles on the top of the sills!
Everything everyone said here makes sense in the bigger picture.
And before Martin chimes in again - hey, mineral vs synthetic saves me a bunch since I have a 10 qt sump!