I previously had a LSE Plasma I on my -6, and they did/do recommend running them on the top plugs. I asked them why once (after thinking about the bottom plug fouling issue) but didn't get much traction on the Q. I do know that making short runs from the ignition coils (often mounted on top of the engine or on the firewall) to the plugs is a desireable state, so perhaps its just easier to do on top.
I recently installed a new Electroair system, and asked Mike there about using the top plugs, as I didn't want to change out my mag harness. Mike said it would be no problem, and it has run very well so far.
One thought I had was that it is recommended (from my install manual) that the EI spark plug wires not be run closer than 1/4" apart, and maybe that is easier to accomplish topside too (it was for me anyway).
Just another $0.02
Cheers,
Bob