The Paladin's entry states:
A paladin must be of lawful good alignment and loses all class features except proficiencies if she ever willingly commits an evil act. Additionally, a paladin's code requires that she respect legitimate authority, act with honor (not lying, not cheating, not using poison, and so forth), help those in need (provided they do not use the help for evil or chaotic ends), and punish those who harm or threaten innocents.
That's pretty straightforward: no evil stuff, no rebellion against legitimate authority, no dishonorable stuff, be nice with the ones in need, punish the bad guys. It could be summed up (a bit naively) as: be a very nice guy.
Additionally there are more precise paladin codes for Paladins of different divinities, which put emphasis on different points. All of them contains the base points of the paladin's code (even if sometimes it's interpreted differently).
The Enlightened Paladin does not follow this code:
Enlightened paladins follow no universal paladin code—each paladin in his service creates his own code.
His goal is to "reach perfection", whatever that means. It's not the same as being a nice guy. It will probably contain stuff like "Always try to be stronger, the stronger you are the better you will be able to punch evil in the face".
Technically the Enlightened still have to be lawful good, so her code can't be "kill everyone you don't like" or it won't work. She also still can't willfully do evil acts. Besides that, the code can be whatever she wants.
There is no ruletext about this new code superseding the classical paladin one, but the fluff text is explicit enough to suppose it was intended to work that way.