Since the Phantom's flight controller is closed source, this is speculation but I assume it calculates it based on the altitude delta from "home".
When you turn the Phantom on one of the first things it does is tries to get a GPS lock on its current position which it will use as the "home" point. This is a pretty important piece of data for the device to have (and the bright LEDs on the arms will light up red until it has it, warning you that taking off is dangerous) because if it goes into "return to home" failsafe for any reason (loss of connection to the controller, battery low situation, etc) the device will attempt to fly itself to that position (after first ascending to a programmable return-to-home altitude if needed to minimize risk of hitting obstacles like trees or houses).
The controller on the Phantoms also has a barometer which can be used for (relative) altitude change readings. I have no idea if it uses that at all in the 400 foot ceiling calculations.
It is extremely doubtful that the Phantom carries any sort of WGS 84 to local height mapping because that is a ridiculous amount of data (even at a fairly low resolution) to carry for the entire globe, and it has no link to any kind of lookup service for that, and if you based the height on sea level that would make the device pretty worthless in many places (eg. Denver which is more than 13 times higher than 400 feet above sea level at ground level).