Bubbling paint means it's more than just a stain. It's real damage, and it requires a real repair - which includes taking the door handle off and repainting the area underneath it because that's where the rust is starting.
This is damage that will not be covered under the factory corrosion warranty, either. Those warranties don't kick in until the metal is perforated. So, it's either get this fixed as a condition of sale before taking delivery, or walk. Problem with getting it fixed is that a cheap-as-possible repair might make it look OK for a few months until the corrosion shows up again.
Good point concerning the sunroof versus the headliner ... those usually start with a blocked sunroof drain (from dust and leaves in the air).
Take-home: don't buy one of these cars sight-unseen ... a thorough in-person inspection is called for, and make fixing this a condition of sale and make sure the repair is fully covered under warranty that covers ALL corrosion, not just perforation like the factory warranty.
$5000 off MSRP is not looking like such a great deal any more.
the salesperson told me the estimate to fix the blue one is around 2K.