The fingerings in the example in the readme are completely non-intuitive for me. I've played piano for a few years and never encountered such fingering. My guess is that the algorithm is optimizing for the wrong metric.
What particular fingering looks odd to you? The only one I see, for the Invention in D, is basically the same as what's given in the Alfred edition of the inventions (and the Henle, and others...).
I just had a look at their example (BWV 775) and the first thing I noted was this: Second finger on the Bb in bar 8 makes no sense (there's no reason to not use the thumb there, especially as the following interval is a seventh).
I hope the internet won't become flooded with sheet music that has bad auto-generated fingering, because it's something that you really trust. If I encounter some strange fingering I trust that the composer knew something that I don't that I maybe should work hard to apply to my own technique, obviously this will damage your technique if it's nonsensical.