Are you actually wondering why people rock in their ponds? It's quite obviously for aesthetic reasons. I refuse to believe that's a genuine question.
As far as it not being natural, well it looks far more natural than a rubber liner. Furthermore, natural rock bottom ponds DO exist in nature. They're not as common as mud bottom ponds, of course. When I was traveling through Newfoundland a few years back on my motorcycle,I remember being taken aback by the many beautiful rocky ponds there. The Adirondacks are another place I recall seeing several rock bottom ponds. Stream bottoms are commonly rocky. Many northern beaches are rocky, such as the Maine coastline, and there are many natural rock bottomed tidal pools there. So, rocking in a pond is a quite natural thing to want to do if you're trying to replicate nature. Sure is not as natural looking as a mud bottom in most places, but it looks FAR more natural than rubber or cement.
In all of my travels, I don't recall ever seeing a natural rubber bottom pond.
I suspect the whole point of this thread is to trash rock bottomed ponds though...
Our main pond has a partially rock covered bottom. The deepest part where my water lilies are is bare. The rocks add way more growing area for beneficial bacteria, and good short varieties of algae to grow. The bog we added is also going to to have a gravel / stone bottom except for near the skimmer. It's a place for plants to anchor naturally. All my mini-cats and mint and iris grow directly in the stone. Larger natural ponds around here have sandy, stony shallows that support all the arrowheads, and bull rushes .... I did my best to make mine based on nature despite the rubber liner underneath everything. As far as I can see, there's nothing wrong with a rock bottom
Edit: P.S. I just cleaned out my waterfall feeder pond for the first time after 3 years of operation. There was some gunk under the stone, but not much at all, but isn't that what happens in natural ponds too? I know most garden ponds are closed systems as is mine, but even with a bare bottom

in you're pond cleaning will still be required, right?. So far I've found that anything that settles into the stone, slowly seeps out and into the bare deeper part of my pond. After 3 years, I still consider myself a noob as there is so much to learn, and maybe I'm wrong about what I said above, but in my short time in the hobby, I've found no issues. I have healthy thriving plants and fish.