I tried out the latest version with an Xbox One controller, but unfortunately it's lacking the ability to Invert the Y axis. There is some option that *sounds* like it but I believe is only while dragging items.

As one of the many people who play inverted this is quite a necessary feature to add, thank you :)

Also, I tried to play without inversion and when I got to my first lock I found the controller much too sensitive to turn the dials. Is that a bug or am I missing something?

+1 for this, searched hoping to find a config setting we could edit.
Hopefully in the works, fun game for sure but old dogs don't want to learn new tricks with a mouse :)