Include the "Primary Parent" checkbox functionality under PSE's "Change Reference Type" dialog in PI Builder
In PSE, you can right click an element reference > Convert > Change Reference Type... and have the option to make your current element reference the Primary Parent via a check box. This functionality is not replicated in PI Builder. Thus, you have to do this in 3 steps:
1) Delete the Element Reference
2) Publish primary parent with the NewParent column set to the path where you would like the primary parent to be
3) Add an Element Reference to the Primary Parent at its new location.
This is a bit cumbersome to accomplish the same thing as a check box in PSE.