There are two things for certain about rocks in the bottom of a pond.
1. They will kill your fish.
2. They will save your fish.
In water garden forums #1 is the most common belief.
On the other hand the world's largest professional pond builder considers loose rocks in the bottom of the pond essential for fish and pond health. They have studies said to prove this as a fact. I'd mention this company's name but I'm not sure of this forum's rules. Some water garden forums in the past have forbidden the mention of their name.
So the choice is as clear as a new pond in July.
Easy solution
The solution is to use common sense. The easiest common sense is to not believe either. The odds are just way better. You'll be right more than you'll be wrong. In the case of this example you'd be right because both statements are so overly simplified that I at least would consider them wrong. However, since both are based on fact they can be debated endlessly as long as science is kept out of the debate of course.
Little bit harder solution
A more complex common sense approach is too believe both. Unfortunately this takes some research, and by that I mean fundamental research on how a pond actually works. If the research is just reading opinions you'll get no where. For example, you might run into something called "wildlife ponds". In these types of ponds muck on the bottom is cherished because a lot of life grows in it which is good food for the fish. These ponds run for years and years without killing all the fish. Common sense might tell you #1 is wrong, and it is.
That might also lead to research rocks being home to beneficial bacteria, but also that these beneficial bacteria can't live when covered with muck. So common sense would tell you #2 is wrong, and it is.
For your case this might be enough. You want rocks, they don't kill fish...good enough.
Informed solution
If you want more understanding you have to research even further. And now it gets really difficult, and this is probably not why you wanted to build a nice relaxing pond.
The answers are really pretty simple. Unfortunately there are competing camps, both intent on "winning" rather than actual investigation. And it's you, new pond builder, that get to sort out the mess.
Rocks on the bottom is only one issue. Pretty much every other aspect of ponds have the same competition for opinions being consider as facts.
The third alternative
Like Captain Kirk you may want that third alternative...
rocks on the bottom and zero muck.. Unfortunately that will bring you to the next absolute truth for ponds
cement kills fish.
When looking for an answer endless information and opinion may not be that helpful.