As someone who worked as a Mac Genius for longer than I'd like to admit, speculation like this bugs me quite a bit. There is no doubt that applying Arctic Silver 5 by hand is going to lower your idle temp somewhat. The same is true for practically any mass produced computer. I can tell you from experience, however, that in most situations it's not going to be worth tearing the machine apart. Maybe a couple degrees. The guy that started this whole rumor with his thread about the first MBPs didn't plug in a temp sensor on the underside of the board when he reassembled it, so his fans ran all the time. Of course it's going to be cooler if the fans are running more.
We would "dev null" these machines for an hour on a hard desktop (running memtest simultaneously, no less) and they would never get excessively hot on the underside and would never settle at a temp higher than the normal operating temp for the processor. There were maybe 2 or 3 exceptions out of 100. I don't call that bad QC. I guess what I'm saying is that these days one person on the internet has a legitimate issue with their machine, but it easily snowballs into a large number of people thinking they have an issue as well. It's a frustrating thing to deal with from the other end, I assure you.