I don't think anyone has been saying that you wouldn't use any of the setting.
But using a setting doesn't mean using all the lore. A setting is, first and foremost (to me at least) a set of maps, proper names, some basic background/history, and the themes that are established by all that.
But does it mean the same thing to your players? If they have familiarity with the setting, are you going to have problems where their expectations and yours don't match up. You see a cool proper name and weave things around it's basic idea, and player X knows about that proper name and it's 80% overlap since you started with the basics but you wipes out this whole section over here that changed how people look at him, and you don't understand why the character treats this NPC like he's a villain.
A setting is also a shorthand for getting player familiarity. Let me use a smaller example. If I say "we're using the Norse mythos" there is a whole boatload of knowledge and interconnections that the players automatically grok. If I say "we're using my homebrew mythos" I need to introduce it from scratch. If I say "we're using the Norse mythos", but Thor is a coward, Freya is they real power behind the throne, Odin is humble, Loki virtuous and there are no Giants - at that point you need to erase more than you gain by reusing something existing.
What you are describing about using bits and pieces of a setting sounds like a movie "based on a book". If no one knows the book you've got a bit of work done, but you've got to introduce everything like it's a complete homebrew without the benefit of using a setting the players already know. On the flip side, if some players do know the setting it's like people who have read the book and are wondering why this subplot is gone, those side characters have been merged, and that main character has been changed. In that case the familiarity works against you.
"So it's Eberron, but the last war didn't happen (""um, I don't knwo where warforged come from"), Cyre is still the Mourneland but now it's inhabited by dragons. Oh, dragons are standard D&D dragons, that whole giant/dragon thing in the deep past was wonky. I've kept eight of the dragonmarked houses, but with changes, and introduced two new ones. There are no lighting rail or airships. And I want the Silver Flame to be pure so ignore the lycanthrope purge and any other oddities. I don't know if I'm using the Lords of Dust."
(And that's only if you could articulate everything you didn't use to the players.)
I don't mind pilliaging settings for ideas and such. But at that point I'm not using the setting, I'm mining a few things from it and filing off the serial numbers.
