To be honest - I don't really know. I never use a tweak such as PKGBackup for backup purposes when I am going from one major iOS to another (i.e. iOS 5.1.1 to 6.1). There is a high probability that tweaks i've been using on the older iOS are fully compatible with the newer. So, I just put my Cydia tweaks on by onsies at twosies after a new jail break - that way I can ensure everything works fine before I go on to the next.
I only use PKGBackup if I am re-restoring the same iOS or restoring after an incremental upgrade (such as iOS 5.0.1 to iOS 5.1.1, for example).
So, there's that.
Marilyn