It's a fact that Miyamoto revealed that a MGS game was in the works for Gamecube. It's entirely possible that this magazine is merely interpreting that to mean MGS4. MGS3 is already a PS2 game in the works so, using some very weak logic, the Gamecube game has to be something different and thus MGS4. My theory is that this is the same MGS game that was confirmed a few weeks ago and it is still unconfirmed exactly what it is. If it's a new game it could very well be a sidequest game like how RE: Code Veronica isn't RE4.
Something that would be really interesting is if Konami released MGS3 & 4 at the same time on two different consoles (PS2 and GC).