I have made a couple UNI filters by hand with the sheet of material and a hot glue gun and ran it with and without the air box on one of my bikes. Personally I like the open end withe outerwears. I currently run a K&N with an outerwear on my T3 and I love it. It sucks massive air so I gotta clean it after every trip but its easy to clean, easy to remove and install, and IMO looks better. I guess it comes down to where you ride and personal preference really though..
My toys:
'84 T3 red Parts bike
'84 T3 green (runner)
'85 Tecate with an LT250r in it
'04 Kawasaki KX250F
Don't blame the ride, blame the skill.