I very much agree with BryonD.
As I see it, there are two kinds of core fluff:
1) The kind that needs non-intrusive editing. This includes things like the Greyhawk gods in 3e, the Bigby spells, etc. Renaming them or dropping them has serious ramifications for dealing with my players. If they know what "Bigby's Crushing Hand" is, they'll know what "Crushing Hand" is. All of these fixed by either not using the thing, completely replacing it, or a trivial renaming.
2) The kind that requires intrusive editing. Things like the Golden Wyvern Adept qualify: I don't want to drop the feat, but I don't want to have Golden Wyverns in my game. I have to rename it, but then I'll have confusion down the line when my players inevitably forget the mapping between "Spell Shaper" and "Golden Wyvern Adept" when they want to look up something about it in the books.
I think that many of the people who don't see the difference must not play with non-expert players that often. In my group, I am the only one with deep knowledge of the rules, and only one other owns his own copy of the books. I regularly have to re-explain Cleave to the fighter. They enjoy the game, but they don't live for it; they don't invest lots of time in memorizing the rules.
Now, I could play a game with them where elves have wings. It'd be pretty simple: I just tell them that all elves have wings, and we're good. However, if I tell them that we're renaming "Golden Wyvern Adept" to "Spell Shaper", and the wizard takes it as a feat, I absolutely GUARANTEE you that he will forget what it means a few sessions down the road, and then be confused when he can't find "Spell Shaper" in the book.
This makes it harder for me to homebrew for my group.