Synthesis of new materials demands structural analysis tools suited to the particularities of each system. Van der Waals (vdW) materials are fundamental in emerging technologies of spintronics and quantum information processing, in particular topological insulators and, more recently, materials that allow the phenomenological exploration of the combination of non-trivial electronic band topology and magnetism. Weak vdW forces between atomic layers give rise to composition fluctuations and structural disorder that are difficult to control even in a typical binary topological insulators such as Bi2Te3. The addition of a third element as in MnBi2Te4 makes the epitaxy of these materials even more chaotic. In this work, statistical model structures of thin films on single crystal substrates are described. It allows the simulation of X-ray diffraction in disordered heterostructures, a necessary step towards controlling the epitaxial growth of these materials. On top of this, the diffraction simulation method described here can be readily applied as a general tool in the field of design new materials based on stacking of vdW bonded layers of distint elements.