physic in editor - to place stones and bake the position?

In theory you could create a separate scene with its own local physics and copy across the objects you want to simulate as well as things these objects collide with. You are then free to simulate the physics on this "sandboxed" scene (in edit-mode) until you are happy the physics have settled, maybe waiting for sleep perhaps. You can then copy the Transforms of the GameObject you're interested in back to the primary scene. You'll likely need a mapping of the Transforms in the new scene to the Transforms in the primary scene for this. You can then delete this duplicate scene.

Just be aware that this'll also call physics callbacks OnCollision/OnTrigger to ensure you don't do anything that'll affect your project in a bad way or is local to the scene.

All this could be done in an editor tool script. I've never tried this though, there may be gotchas I've not thought about. Certainly simulating the primary scene in edit-mode can be dangerous as everything is simulated and things like joint-breaking that destroys joints execute so you'd find components being destroyed so be careful with that.

 

You can use Instantiate to clone any GameObject and its children. These clones should be put into the new scene where you can simulate them.

Note that there's also the option of using a save playmode script (think there's something on the asset store and I've seen some examples floating around on GitHub) to persist the Transform values in play-mode.