An extended set of coupled wave equations were derived to describe non-idealized lamellar multilayer grating structures with properties as obtained with state-of-the-art fabrication techniques. These generalized equations can include all relevant effects describing the influence of passivation and contamination layers, non-rectangular lamel profiles and sidewall scalloping. The calculations showed that passivation and contamination plays an important role in that it may significantly reduce peak reflectivity. However, we also derived a condition for layer thicknesses having negligible effects. Slightly positive tapered lamel profiles are shown to further reduce the bandwidth as compared to a rectangular lamel profile, whereas negative tapers significantly increased the bandwidth. The influence of intriguing effects, such as the sidewall scalloping caused by Bosch Deep Reactive Ion Etching, are also modeled. We identified the signature of such scalloping as additional side peaks in the reflectivity spectrum and present parameters with which these can be effectively suppressed.