A bit of background. Autotune feature was initially introduced back in OpenPilot before split of TauLabs happened. You can see that in old GCS movies. Then OP removed Autotune (probably for safety considerations), but TauLabs kept it. I can imagine it was not considered to be safe, for users who have no knowledge of PIDs tuning, but tried using it. Of course Autotune, improved over time, and each team added value to it.
Now it is back in LibrePilot. It is automatic process but in my option it does not remove burden from user of knowing what PIDs are, and how the process works. It may work for everyone else, but you might be the lucky guy from FTT discovering case when it fails miserably. I advice to always check PIDs before flying them, do they make sense for your build ? Be aware that this is development branch of feature that have just been added.
For testing you should use Attitude mode both for tuning and flying. There is a chance that oscillations can make quad climb even at very low throttle, requiring to stop motors, let it fall, recover (repeat) to get it down. Also try to take off with new settings instead of switching to them in flight, to get a feeling how new PIDs work and be prepared to stop it. Another recommendation is not to use big props that put your motors on the edge of power rating. If motors can stand full throttle for long time you should be safe. This is important in case of micro-oscillations, which can make motors hot. Even if the PIDs look reasonable be careful the first time you let props spin with the new PIDs. Bad PIDs can cause oscillations, and that can cause a very low throttle setting to act like 50% throttle, likewise high throttle can become 50% as well. Some oscillations can't be seen or heard, but you can tell they are there if it feels like all throttle settings are closer to 50% than they should be.
All feedback is of great value for further improvements.