It makes a lot of sense to me. When an additional optical element is introduced, the way that the light converges at the film / sensor plane will be affected as different wavelengths of light travel through glass at different speeds. The old lenses were designed to ensure that the rays converge at the film plane.
Add the optical stack and all of a sudden this does not happen any more and the different wavelengths of light will no longer converge where they were designed to, i.e. at the microlens position. This is going to be especially apparent in fast, wide angle lenses more so than longer, slower lenses.
I'm a little surprised that the Sigma does not have some level of protection in front of the microlenses. There is obviously no need for an AA filter and
I guess the IR / UV filter could be integrated into the layers of the sensor.