Ryan, morning... I looked for a manual on-line to try and find that "warning"... can't find a manual.....
So..... I am going to assume (that is bad) they are talking about lining the racks with foil.... The possibility of creating a "heat block" by sealing off a rack completely and overheating a section of the smoker could exist... When operating any kind of oven or smoker, air circulation is very important and probably at least 25% of a rack should be left open for proper air/heat flow... (I just guessed at that number)...
That is of course, not even thinking about some idiot that sued them for something to do with aluminum foil and won the suit....
Now to your question.... Foil 'em....
Dave