I'm going to take a wild guess that this is your first foray into the off road world. The holes are pretty minimal and put there intentionally. Some provide access to things like drain plugs for oil. Others provide a little help with the heat generated by the motor and transmission above it.
The factory skid plate isn't much of a skid plate though. It really does more to keep small sticks and small rocks from being thrown against the expensive parts above it than it does to slide the belly of the machine over a rock ledge or log or an impact. If you stick to mostly well groomed trails, dirt roads, forest service roads etc it will do the job. If you start getting into ruts or ledges or rocks or other belly dragging/smacking items then you would be wise to get an aftermarket skid plate ordered and installed prior to learning the hard way it wasn't adequate.
Welcome to the club.
Pics or it didn't happen.
Red is the fastest color.
#NTC