Neil Young is a sharp guy! He is absolutely, positively, on-the-money right. Rust Never Sleeps. A good album. And the truth. The good news is that not all rust is the same. There is rust. There is rust. And then there is RUST.
Rust: Occasionally we come across vehicles that have mild rust. You know, stuff like rusty spots where the paint has chipped, and maybe a couple of spots under a window seal. Rusty paint chips are nothing at all, really. They are wide open, so capillary action cannot feed the rust more moisture. Thus, rusty chips typically don't spread. Window seal areas are a different matter. There is quite a bit of capillary action going on there. But it is totally manageable and essentially inconsequential. You can simply remove the window and clean off the rust, or cut it out and replace the rusty metal with a clean, fresh patch. Prep it, paint it, and voila!
Rust: Every once in awhile we get a vehicle in from a notoriously rust-prone part of the country, like the midwest or the northeast. Sometimes they have such low mileage and/or are so new that the rust simply hasn't had time to really take hold. Perhaps there are some rusty suspension components and fasteners. There might even be a fastener or two that has to be cut off. But still: quite manageable. Once the rusty part or fastener is removed and replaced, voila! Of course, it can be expensive to replace these parts, but still quite fixable. It still hasn't moved into the following category...
RUST: Now we're talking rust. When a vehicle has been in a corrosive environment for too long or for too many miles, you get RUST. Now we're looking at some serious holes in the vehicle. But, still, even holes are repairable. But rusty seams... rusty seams are a bitch. Once the seam loses its outer caulking seal, moisture gets in and you've got RUST. You can never get rid of rust in a seam. Well, you can. But it would mean cutting the body apart, replacing all the material that has been affected, and welding the body back together. So, yeah, anything is fixable. But not all things are feasible to fix. Sadly, the most feasible way to deal with seam rust is simply to keep it at bay. All you can do is scrape out the seam as best you can, blow in some rust inhibitor (wear your safety glasses!), cross your fingers, and hope for the best. If it is not too bad, you can re-seal the seam and paint over it. But, depending on how corrosive the environment is where the vehicle is put into duty (proximity to the ocean or salted roads), it is just a matter of time before it comes back. The good news is that seam rust is rarely a structural problem; rather, it is an aesthetic one. Shoot, some of us are even proud of our seam rust. After all, we get tired and have to go to sleep each night. But our rust never sleeps...
The bad news is that regardless of whether you have rust, rust, or RUST, there is no permanent, fix-it-forever cure. Keep in mind that when VW built the vehicle brand-new, they had the absolute best circumstances: All new steel, perfect welding conditions, and so on. Still, the vehicle ended up rusting. The best that can be done on a 20+-year-old vehicle still doesn't hold a candle to what VW did when it was all new. Basically, it is unreasonable to expect rust to never come back—especially if the vehicle is driven in harsh conditions and/or where there is salt on the roads. The rust will come back—it's just a matter of when, not if.
Rust just does not sleep. Ever.