The only thing I can think of is that the below the lens versions are held flat by plastic frames where as the above lens one are not, so you would have to construct some type of holder that would keep them totally flat or else they could droop and cause optical defects.

When I used them, I needed larger ones for my 150 Apo N so I made a holder out of a Cokin gel holder and it worked great with the small above the lens set. I now no longer use them because I replaced that enlarger with an LPL 4550XLG with the variable contrast head...