IF the repair is done properly by a qualified individual, you might be satisfied with just the repair. I'm sure Harley will insist that you let them try that first, and I'm equally sure they won't cave in immediately and send you new engine cases. Now if the repair doesn't work, you might have justification to ask for a case replacement.
Don't be too eager to change the engine cases btw. Are you really sure you would want that dealership with the constantly changing staff to remove your engine, completely tear it apart, pile the parts on a grubby workbench, put the parts into the new cases, and then stuff the engine back into the frame?

As for your question about others having this problem, I remember a lot of folks in 2009 having peeling of the case paint, in some cases very severe. I've seen complaints pretty much every year since. It's just one more sign of how little Harley management cares about really fixing quality issues. While you might think spending nearly $40k for one of their products would entitle you to decent quality and customer service, I've seen no evidence that Harley thinks the same way.
Jerry