The very limited depth of field of a microscope necessitates doing depth stacking for every field of view. This is done automatically by the apparatus. As a side effect, it gives a heightmap, but with the lens used for the whole-painting scan (what HIROX calls "35x", corresponding to ~5 µm sampling resolution), the elevations are not reliable, especially near the edge of the field. For selected areas, a higher magnification was used that gives much more reliable elevations. Sadly, only a small fraction of the painting was imaged using this higher resolution, so the 3D data is spotty.

Very likely. The focus stacking software (such as Helicon) can output the 3d object in addition to the stacked image