I added a strip of fiber-glass cloth across the bottom while the covering was off gluing up the bottom fairing. I figured how could it hurt. I can see where the side mounted motor would make life easier, if ya don't mind it sticking out the side a bit. It'll run cooler anyway, inverted is strictly an appearance issue. Upright and inverted are a little better for lateral balance too, even if you balance laterally the moments are usually different as the weight is usually out on the wing. Not usually an issue in 3-d however, and a very subtle issue at best/worst.
One guy at our club who is a very talented 3-D flier always leaves his cowls off on 3-D craft. He flew his Funtana and now his Flip 3-D this way with the engine upright. Never seemed to cause him trouble what so ever, I could even see him mounting the engine upright through the cowl, he's that kinda guy. It'd be easy to give him grief about some of the other contraptions he brings to the field ..that is until he gets them up into the air and makes them dance. Then I just start calling him Master Yoda and telling him how I want to be a Jedi someday too.