Any weight will affect vibration in the chassis which will affect microphonics which is a known cause of sonic change. This could be waht is heard with a Shkti stone and would be hard to separate from the claim of electro magnetic affects made by Shakti. Perhaps both affects occur.
The critical thing is do you really hear a sonic change and if you do, do you like it. Knowing the cause scientifically is great and reassuring but too often we aren't granted that knowledge. That's why audio is both subjective and objective.