I don't like it either but it feels like the type of thing that would never sound good if you're hearing it clearly. The fundamental frequencies and all of the overtones have to shift, in theory, without changing the timbre. I don't think that's even possible. I imagine it could be passable in a mix for a covers band with one or two Eb songs in the set. Over the years I have gotten so picky about being in tune and intonated, I set up one guitar per tuning I intend to play. The hassle involved with that has let me to stop playing in other tunings as much. I don't even like to tune to drop D for one song because I have to compensate on all the other strings and then it's not intonated because I'm not going to bother with that for 5 minutes of playing. Given all that, I could see using it if I was in that situation, even if I didn't love the sound. An audience with one or two beers in them probably wouldn't notice anything wrong.
Fractal's choice here might be something like: include a feature that will please some people or exclude it because it won't please everyone, and then it's easy to see why it's in there. I'd be interested to hear if the AxeFX III version is satisfying to people who use it in a way the FM3 isn't.