It does negate dual channel, yes. But Dual channel generally only nets you about 3-5% performance boost, so it is more in the realm of the "It's free, why not" category of things you can do for your computer.
The reason, I imagine, that they are putting 3GB in the systems is because it is more than 2GB, but less than the 4GB system RAM limit imposed by 32bit Windows (and most all 32bit OSes). They don't put 64bit Vista onto the systems, so instead they put 3GB of RAM.