No matter if you choose to include the 3D effect or not, your end result is influenced by how you position the two lamps, and thereby the angles of how the light hits your original during scanning.
The four options for lighting are made possible by the easily accessible levers on each side of the scan module moving the two adjustable lamps. Each lamp is with dual LED strips mounted in elliptical reflectors. LED spectrums are 2,700K/ 5,000K/, 6,500K and the museum-correct light with no UV/IR radiation uniformly illuminates in all three dimensions, while the scan module shields off ambient light.
The ‘Illumination’ setting in the software indicates where and how much the highlights and shadows will affect the result – depending on how you position the lamps:

Even without the 3D effect enabled, you can get a subtle shadow and highlight effect by scanning your original with the left lamp in the ‘up’ position, and the right lamp in the ‘down’ position. This gives the image an instant look as if being lit from above.
Here it’s a small section of the blue and yellow test painting, scanned in 600 dpi with the lamps set that way (up/down):
