You may want to modify a Waveform referenced by a Cue or a Timeline without changing its settings.
For example you may want:

To replace temporary data with the final data (such as replacing a dialogue line)
To adjust the Waveform by applying an EQ
To apply more reverb
In these cases, it would be troublesome to have to register a Waveform again from scratch.
In AtomCraft, you can update the Waveform by directly modifying the file referenced by the material in Finder (Explore).