Actually I think it may be slightly undertracked too (for reasons I'll get into later), but it is essential to realize that the 3 million is a shipped figure, and VGChartz reports sold to consumers figures. Let me say that more simply.
Konami has announced that they have sold 3 million copies of the game to retailers (Amazon, Wal Mart, GAME, etc).
That's a lot of stock in the channel, though. Just from a purely shoot-from-the-hip standpoint, having 1 million copies in channel ("in the channel" is a term used to describe a game that retailers have purchased but they haven't sold to consumers yet) is a lot for a game that has thus far sold 2 million copies. It's not impossible, of course, but it's a lot.
We'll see, though.
Well, not to long ago Take Two announced having shipped 11 million copies of GTA IV while selling 8.5 million copies to consumers at the end of May. If GTA IV can have 2.5 million copies in the retail channels after 5 weeks on the market I don't see why MGS can't have 1 million copies in the retail channel after 2 weeks.