Well, the lightning rail grows out of elemental binding, which grows out of the existance of both elementals and the existance of magic items (sounds like a Civ-type tech tree

).
The alignments aren't really changed. You can have evil gold dragons, good vampires, and the like (though outsiders are still more likely to be of their alignment), and clerics don't have to be within one step of their god's alignment (opening the potential for hard to detect corruption*).
*Since, by the rules, an LE priest of a LG deity still radiates a good aura!