From a structural engineer's point of view (not automotive) I can see no reason chassis rigidity would be affected either way. If there were any flexing in the area of the moonroof, you would hear creaking in the area between the roof gasket and the glass panel.

The 3-series is one of the most rigid stock automobiles available (perhaps THE most). Chassis rigidity shouldn't be a consideration in whether or not to opt for the moonroof, IMHO.

I'd guess the moonroof delete would save you about 15-20 lbs. Each seat, probably another 15 lbs.

I'd estimate total weight savings would be around 50 lbs. That is significant!

John,
I am not disputing your stand on this but i do remember from my Bachelor level Physics that it's the flexibility of a metal that determines it's strength, for a stronger body you would want more flexible metal. That is why steel is used which is the most flexible. As far as i know flexibility of any metal is described as the ability to come back to it's original shape and thus resist deformation, a concept opposite of rigid bodies. You would'nt want to construct your car of a rigid structure. Young's modulus.