The factory ones often leak.
It's a large vehicle shaped like a brick with removable and interchangeable doors, a hinged windshield, and removable and interchangeable non-motorized tops.
When you have a soft top and half doors, the entire upper half of your vehicle is essentially kept from the elements by a relatively inexpensive, glorified, multi-piece tent.
"No leaks" is something you hope for, not something you're realistically guaranteed.
At least you have the factory warranty with ones you order from the factory, so if there are leaks you can try to get them fixed for free.
But honestly, I always planned on going with rubber floor mats and pulling the carpet out of my JK, and I'm glad I did. During big rains, some water comes in on my passenger side floor and I don't care. It dries on its own or I wipe it up.
JK ownership is less stressful if your leak concerns are limited to large, cascading amounts of water rather than the occasional damp floor.