Dear, we need to know if TOAD's object comparison tool works efficiently comparing wrapped objects
Honestly, I don't know.
It does not unwrap anything. At best, it will compare the wrapped code, and if it is different, migrate the wrapped code from source to target in the sync script. It won't be able to deal with spaces and formatting the way it could with unwrapped code.
It should be easy to test though. If you test it, let us know.