So if anyone is interested in the second half of my post, I've attached a VI that does what I was suggesting. It takes a list of Installed Files which the Post-Install VI can return. Then for all Libraries and Classes it looks at the members, and find where they are on the palette and finds the most root MNU file installed and sets the default menu to this palette. So for instance if you have a palette with an Advanced subpalette, all members in that Advanced palette will actually point to the root palette when you right click which is think is a normal work flow since the right click doesn't give bread crumbs to navigate up, only down.
I intend on using this in my package building instead of the built in function because of its support for multiple classes and libraries within a package.