My guess is S&W only Melonite treats the bare slide and the barrel only. Parts like the take-down lever, slide stop, guide rod, etc. are not treated. I could be wrong though. Is the actual slide and/or barrel itself showing any signs of rust (I sure hope not)? If you find out from S&W that the other gun parts besides the slide and the barrel are not Melonite treated as well, I would talk with Robar in AZ and see what they would charge you to NP3 the parts (that would do the job on stopping the rust on those parts).
Just read your last update. Wow, the actual slide is showing some rust. Yep, get S&W on the phone as soon as you can and explain what is happening, maybe you got a M&P that slipped through the cracks and missed out on getting the Melonite treatment process somehow. Strange.