No, you should not use substrate in a hospital tank for the reasons stated above, and yes, the bare-bottom reflections will stress fish out. To avoid this, you paint the bottom of the tank [on the outside always] black. You can additionally paint the back and sides. Also, yes, you do need comfort zones for your QT or hospital tank. Many use PVC rather than rocks, because rocks tend to absorb the med and, also, harbor the diseases. If you use rock, just make sure that you do not place that rock back in your display.