Okay... that makes sense. I really don't know whether it would do stereo track alignment but again, since it seems to be aligning one waveform to another I can only assume it would be able to do one mono wave to another (and still be accurate). So again I'd say just split the stereo tracks and do it once for each side.
However if you are using a stereo based effect that may cause the waveform's transients to be REALLY different that may cause a problem.
Also considering how compressed a lot of guitar signals can be I'm not sure it would even work for things like distorted guits... because if all you've got is two flat, compressed chunks what's it gonna align things too?
For more dynamic clean tone I'm sure it would be alright but really without getting my hands on it I don't know. In the vid they said to try it on stuff other than Vox but that the results may vary so I'm assuming they've tried that kind of thing and it was unpredictable. Otherwise I'm sure it would have been promoted as more than a vocal tool.
Anyway, that's a long way to say... IDK. Lol... sorry.