As others have observed above, the two flange screws are intended to hold the case in place, and for most CoolerMaster plates this does work. However, I have noticed that those bent plates edges (particularly in the MasterKeys keyboards) aren't made to particularly tight tolerances and as a result, some folks may see a bit of movement in the plate, even after the flange screws are fully installed. The solution, as some have said, is either to put a piece of paper between the flange screw and the plate or to lift the plate up a bit by putting a long strip of shelf liner on the little "shelves" where the plate sits on the edge of the case bottom. I found that I liked the second option better, even it required a bit more work. I'll fix this for round 2 by deepening the pocket in which the flange screw sits to account for the observed variability in plate heights from CM.
In practice, for whatever it's worth, I consider the flange screws optional, since inertia generally keeps the keyboard in place. You have to intentionally introduce side-to-side movement by grabbing one of the keys hard between your fingers and trying to move the plate. Of course, this doesn't happen in normal typing. Indeed, my first prototypes didn't include the flange screw feature and I used one for months that way without any problem.
EDIT: Oh, and incidentally, another feature of the flange screws is that they make it easier to assemble the case for the first time. They prevent the plate from falling down out of the bottom of the case when you have the keyboard flipped upside down and are assembling them to be screwed together.
