Well, to be honest, I do use PKGBackup when I restore/re-jailbreak my iPad (to clean it up). It's just too much work, for me, to put everything back the way it was.
If you remove the tweaks and repos you don't want OFF the iPad BEFORE using PKGBackup, then it'll work out fine ... at least for me.
PKGBackup really only reads/stores/backups existing tweaks. Then, on a restore, it only puts those items back on.
Well, that's what works for me...
Marilyn