I would suspect you can do most of those things to make your setting unique. For instance:
"I don't want Star Pact Warlocks in the campaign?"
How about creating your own warlock class, and not including it, then directing people to that class as per the suggestion on Humans above.
"Healing magic is weaker, so all healing does -1 point?"
Add a new effect, call it the bane of healing, have it add a -1 penalty to damage healed and apply it all the time.
"I want Raise Dead to be more difficult, and not available until higher levels, or to not have any cost, but rather a quest component?"
Same as with warlocks.
"Want Eladrin to lose their teleportation ability in exchange for something else because the Feywild was destroyed in that campaign world?"
Same as with warlocks.
The only part of this I think we actually need clarification on is the omission of the original reference so that your new creation can replace the old, if you need to swap out.
I might have to do that warlock one, by the way. It's completely a flavor change, though, so maybe it will pass. We'll have to see how they define fluff as it interacts with references.
Actually, now that I think about it, I just have to define what the stars actually are, which I don't think IS defined, so doing that is no change.
However, that's not really an immediate issue.