The plastic is clear because you can see through it. Tripping, falling, or kicking the trap is usually eliminated. Black plastic obscures your vision-- you might stick your head up at exactly the wrong time. Getting blasted in the face is waaaaay down on my list of Fun Things. You can always cover the clear plastic with something dark afterward.
I NEVER carry the trap by the handle unless it's empty. It's bad enough with a scared feral cat lunging from one end to the other. A skunk??? NO-NO-NO-NO-NO!
What's the point of keeping it calm with black plastic and then shaking it up?
Sue