2013 Jeep Grand Cherokee - holes in the bottom

While vacuuming my Jeep I noticed that at a certain angle
I could see the street through a hole while looking
underneath my passenger seat.  I panicked and went to
Autozone who could not help and then to the dealer
where I had 4 guys viewing the issue and we came to
conclusion a plug was missing.  Plug is now on order as
dealer did not have it.  Once home I decided to google the
underside of my Jeep because I crawled under it myself
to see the issue.  There are several holes at the bottom
and some have plugs and some don’t.  Comparing this to
the picture on google it seams these plugless holes are
meant to be there!?  How can this be?  Why where these
holes built in a way that water could get into your Jeep
easily?  Mind you no water has ever come invite but why
these holes and would it be better to plug them?