Definitely can run the Excalibur with less than the maximum number of trays.
The Excalibur really is quite brain dead simple in construction.
Simple slots to slide in the trays...nothing more.
As I am only using this for my backpacking meals and drying fruit from time to time (not a heavy user at all), I will often only use 3 of the 5 trays that I have.
Plus for "taller" food that would hit the tray above it, being able to remove a tray helps.
Thinking back, the only time that I might have rotated trays vertically is if I had all the trays going....even with the heating element being at the back of the unit, the top trays would dry a little slower. Possibly as a result of moisture/humidity of the food from the lower trays rising up and saturating the dry air...heat rising = little slower drying on the top most trays?
I will say that in terms of using it, little noisy, but not too bad. Does not put off any heat at the back and the hot air is vented out the bottom of the front door.
Not hot enough to damage anything. Top of the unit can be warm to the touch, but again, nothing to worry about. Heck, would make for a nice way to dry out a Platypus water bag/bottle by tossing it on top of it while it is running for a slow drying? :)