Hi, currently the position of the new clone is hardcoded in meta-box/js/clone.js
file as you can see here:
http://prntscr.com/duj1eg
The group extension doesn't change this behavior.
For now, the only way to change that is changing the code directly.
I'm thinking about adding a new option to Meta Box to reposition the "Add New" button and the position of the new clone.