The Audio Chord Wizard is fine for very simple chord progressions, but throw an audio file with slash chords, or chords higher in complexity than a seventh and it really does not work well at all.
I have only done a few songs. You are certainly right that as the chord complexity increases, the wizard is less accurate -- or at least comes up with chord spellings that are less and less like what a human would do.
In my case, I rarely do "cover charts" where I am trying to transcribe literally. I usually intend to change a significant percentage of the chord anyway, so I like the fact that the wizard gives me a pretty quick way to set up the song structure (marking measures, blocking out sections) and getting enough chords in there to be a good starting point. Maybe I will tire of the process after doing it a few times, but so far, I think it does enough to be useful to me.