Your perspective has the unfortunate bias of being posed at the end of a long stream of evolution that happened to emerge with an intelligence far superior from other living things.
> Considering that the experiment is run at planet-scale over billions of years
It's not just planet-scale, it's universe-scale. Lots of planets conduct the experiment, ours just happens to have resulted in intelligence.
> It's hard to believe that it's truly just random "bit-flips".
Mutations introduce randomness but beneficial traits can be selected for artificially, compounding the benefits.