Thank you for the response and clarification Deltakosh 
I’ve been banging my head a bit more since I just can’t figure out what is happening in my game, but I think it has something to do with the parent. I updated the playground as well to explain a bit more.
https://playground.babylonjs.com/#S7E00P#98
The two black rectangles now represent the way the pieces should go to, but the pieces seem to be mirrored x-axis wise even though they are given the right coordinates… I think the instanced mesh was actually working “better” without the parent. Is it doing something wrong now?
Here is a reference picture as well… Does this have to do something with the left handedness?