There must be something else at play, as the backup I restored from was only 2 days old and had been generated with Cydia 1.1.1 already in place. The backup should have contained the new addresses. The few mentions I have seen of this issue imply that it wasn't just the addresses but the way they are handled that has changed. I have also seen references to the problem that indicated that Merge may pork the default addresses as well. The only "safe" path seems to be to avoid selecting the default addresses for restoration.
I do not know the mechanics of repo addressing or how they are handled by Cydia or Pkgbackup, but your scenario of what I did above has some incorrect assumptions and seems to oversimplify the root of the problem. I'll be curious to see if there is more info in the coming days.
Cheers!
sn0wbreeze 2.5 JB on 4.3.1 iPad 1