As far as I know, there isn't any way to change the player's reference and it's a hard-coded aspect of the engine. If you open up the Creation Kit but don't load any data files, you'll be able to see that the player object (hard-coded with formID 0x7) is already there, apparently with a count of 1. The Creation Kit doesn't seem be entirely functional without any data files loaded, though (for example, nothing shows under "All"), and I can't find the player reference here.
The player reference can be found once Skyrim.esm is loaded, though. For example, if you set up a condition using GetIsReference you can use the filter to find "PlayerRef", with formID 20 (0x14). As far as I'm aware this is hard-coded and will never change. If the player appears to change into something else (like turning into a werewolf or vampire lord, or like when you
Spoiler became a child in a fantasy world
in Fallout 3) their reference doesn't change, but instead the player's data (like their race) is manipulated.
Of course, I could be wrong about this, but unless someone has encountered a case in which the player's reference changes or a dev can weigh in and say that I'm wrong, I'm pretty confident that this is correct. Confident enough, at least, to rely on this assumption in any mods that I would create and release.
Cipscis