Haha, but they aren't compressed that much, if they are filling up all the space. Textures, sound and video's I'm guessing aren't that compressed, hence the installation before you can even play most PS3 games.
Look, this takes place during a flash back section. That was where snake was entering the blast furnace in MGS1. At that part, otacon tells you to change the disc in the PS1 version. You can interpret it as poking fun at the 360, but really all they are doing is poking fun at the fact that they changed discs at that point in the original MGS.