So IMO if you are looking for packaging/scripting for a single EXE (like package builder), I would use Inno Setup and Inno Script Studio . Very much like PB but better.
I have not used the limited edition in a long time since we have the full version. However the website indicates that only capture and Tuner are included. So you can do snapshots and transforms.
So you could combine the two for free. Use admin Studio, orca, Insted, or others to create a transform and use Inno Script Studio to wrap it up and run other exes scripts and make changes. Good art of this it is all free.