Industrial computed tomography (CT) is a proper tool for extracting both internal and external geometry in one measuring procedure without destroying or rebuilding an assembly. The diversity of assemblies and unique measurement requirements demand an expert user to be able to determine appropriate CT setup parameters. Recent publications have concentrated on the automatic choice of the CT setup parameters or on the determination of features to qualify the chosen setup parameters. Setup parameters consist of X-ray source parameters (i.e., voltage, current, and exposure time), a number of projections, a source-to-object distance (SOD), and an assembly orientation. For multi-material assemblies, it is advantageous to combine two different energies from one or two X-ray sources. Benefits of this combination are a reduction of artifacts, caused by a high absorbing material, and a increased resolution of the CT acquisition (i.e., the combination of high-voltage and low voltage-micro targets). On the basis of previous works, the assembly orientation depends on other CT parameters and requires a correction between measurements with different energies. However, to avoid additional uncertainties due to the fusion of CT volumes, the assembly orientation in the CT system should remain constant for both of the measurements. This study considers the independence of the best assembly orientation tendency and X-ray source parameters. To test the concept, the authors produced CT acquisitions of a multi-material assembly (a polyoxymethylene (POM) cube with two aluminum cylinders) in four different assembly orientations. The choice of assembly orientations was based on the sorted list of minimal required energy. The two sets of X-ray setup parameters that were chosen for the experiment were maximally distant from each other. The concept was validated by statistical analysis of the standard deviations on 48 features of the assembly. The results demonstrated that the group with the best assembly orientations is independent of the X-ray source parameter sets.