The project datum is a false 0,0 point that Muk3D uses to improve the accuracy of calculations. To set it, load some topography, run File/Project datum/Set project datum and Muk3D will grab the lower left corner of the dataset and use that as the origin when working with data in the project.
From the user perspective nothing will change. All data is still shown in the correct coordinates and all exported and imported data will have the correct coordinates.