The process is quite simple, but wasn't as bad as some i've seen, I should have taken some before and after pictures but I didn't think of it at the time.

The only rust on mine was on the outside the inside was as good as new. I think one of the reasons for the rust is water ingress through the spoiler (mine has the fixed spoiler) as you mention, When I bought my car about 6 weeks ago, I noticed the seal was not seated correctly, so this was the very first job I put right. I also had water in the boot floor, but the water was very clean and so hadn't been there long, I put it down to the dealer valeting the car (although not to my standard ). One thing you will notice about these cars when you start poking around underneath is that Mercedes put drain plugs all over the place. The other thing I noticed about this area is the metal is very thin (less than 1mm) and very sharp, I think this adds to the problem because the paint doesn't seal the metal and leaves the edges exposed.

So, back to getting rid of the rust. Firstly I scraped the surface clean with a blunt chisel, I then rubbed it back to clean metal with 240 Grade paper, then moved up to 800 grade, I then used primer filler to build up any inconsistencies, flatted that black primed with grey primer, flatted back again, then I applied about 5 light coats of paint, allow to dry between coats and flat back if necessary the paint will look lighter than the surrounding area, don't worry it darkens when you apply the lacquer. I applied about four coats of lacquer, allowed it to dry over night and then flatted it back with 2000 grade paper and compounded it and finally polished.

Simples ......