prestiege classes are classes that require you to join an organization, do some quests for them, and get special secret training allowing you to be more powerful than if you took "base" classes (which has no prerequisites).
Your class levels, base or PrC, are not fluff...
that is, a fighter or a barbarian doesn't know they are fighter or barbarian, only that they hit things with a sword...
What you describe is interesting fluff, but you mentioned nothing mechanical about it.
Now, some fluffs require mechanical changes. For example, playing a one armed wizard who wants to still all his spells (without horrible penalty) would need a custom class feature (to avoid the +1 level on all your spells ever penalty).
But what is it mechanically that you want to do that you can't do already?