This is very similar to an earlier post here about flying over a canyon.
Since I am a newbie to all this, I'm wondering how my new Phantom 3 Standard will react to this situation. If I take off from a cliff and then rather than go up into the sky above I want to explore the cliff face below the take off point and fly out over the ocean at a lower altitude than the original takeoff point. Would there be control issues with the P3S becoming confused with its positioning operating at lower altitudes than the original takeoff position?

This problem was thought of by the DJI engineers when they designed the aircraft. The aircraft will not be confused at all, it will simply show an altitude in the minus range. So if you flew down 30 feet below your take-off point, it will be shown as -20 feet.

And in case you were about to ask, no it does not confuse the RTH either, it functions correctly.

Thanks for the quick response. Good to know. I plan on being at a location I can do that soon but was nervous about it.