Didn't somebody say that a Mazda tech mentioned they didn't offer the sunroof because it interfered with the air flow to the rear spoiler? I hear you on that though...I wish I had one too.
They didn't put the sunroof in the MS3 because the center body frame sits in the same spot and it's effective for the body handling. Putting in a sunroof would affect the handling and the airflow like chacon101 stated.
adding sunroofs big holes in roof of car can lead to more body flexing thats the reason for the lack of sunroof. and yes the rear windows go all the way down.
And the Corvette Z06s (2001-2004, 2006+) are not available with a targa top or convertible as the base Vettes are. At least with Vettes, they would stay hardtop for chassis rigidity/handling reasons.