Saving custom binding is definitely another area I need to look at. Not even all of the important settings are saved in the current version (bindings are, but not toggles/inverts/sensitivity/scaling)
I do have plans for alternative options to player prefs and I've even coded other save systems that I could probably pull into Sinput with very little work.
Update: Sinput now saves all of it's settings as well as custom binding, and on PC it writes to a file instead of Player Prefs too. :)