Depends on the size hole. If it's small, just a drill spinning at high speed. Then, an exacto-knife is used to trim the "poke out" you observed.
If a larger hole, I start out with a drill, then use a dremel tool with the small sanding wheel to clean it up. After, I use the exacto-knife to trim any poke-out.
TBH, I don't spend too much time making it look pretty because the first time out, the shell gets messed up. Maybe I should learn to keep the vehicle rubber side down?