Setting the defaults works fine, the only keys that would need remapping at the R, Z, and L triggers depending on how you like them, and those have no issues. I would recommend putting a warning sign in the device compatibility master list regarding the nyko suggesting not to remap the analog stick and just leave it by default.
And yeah, I've read of people saying it broke their bluetooth functionality too. Thankfully it didn't break mine in a Galaxy Note 3. Their app is pretty much pointless too, because it doesn't do much anyways. (besides breaking your phone and crashing all the time)