Yea youre right. The referencing through another layer shouldnt make a diffrence in that.
I made an interestig observation.
I made a stack of boxes and placed 9 under a First as a child by accident instead of making an empty.
That made no diffrence with a physx stack.
But a Stack made with newton Bodys it behaves diffrently. One Cube stayed in air before sinking and then made some crazy moves. So there is a diffrence when a newton body has a newton body as a child. That behaviour is definitve reproducable. The body of which the other where the children behaved diffrently and stayed in air instead of normal falling. And when multiplying this by putting it under another some more levels things explode ;D There are no joints or other things in play so its only the gameobject children connection in place.
That might even explain some of the car issues we got with the floating and getting in air???