Just like every newly-built house have a leak or two (-- even that is when you're lucky.), I believe every new Airstream (or any other RVs) have a few leaks. Even when you think you have a perfect house or a trailer, that probably means that there are leaks unbeknown to you. That may be worse.
The factory does put the entire shell into a "rain-storm" bay to test for leaks and fix them before they start building rest of the interior.
I've been on the factory tour a few times, and it seemed that the nice friendly hard-working people at the factory do make their best efforts to create a good quality products. I found nothing that would suggest otherwise.
Having said that, there are so many rivets, screws, seams, and caulking. And all it takes is a few tiny tiny breaks or delaminations among out of so many potential spots, and you have leaks in the trailer.
It can be been almost 2 years since your trailer left the factory, the effect of UV in the past year, and the shipping and delivery to Floridawould its road vibrations would probably cause on your AS some few spots of caulking failures...
I think it's just matter of luck whether the leaks result in minor or serious damage.
Just like anything in life, I think AS needs the vigilance of the owner to keep it in good shape.
Without seeing pictures of your "stains", I don't know how to judge if it's minor no-big-deal incidents or damages with serious consequences.
Is it possible residue stains or water by the window on the walls are from condensation? 3~4 people sleeping overnight more than likely to cause drips on the wall in humid weather.
Skylights are easy simple fix. I would prefer not to have the warranty to replace the skylights with the same ones. It would crack again in a few years anyway.
Classic should have same aluminum interior skins, and I don't know if the interior wall paddings are kind of materials that would soak water.