I think there needs to be some clarification here, since people have some incorrect ideas about how Valve deals with bundles and extra copies.
Steam used to break apart bundles. It is the reason I have giftable copies of some games. They stopped doing it maybe 6 or 7 years ago, but I remember that it use to add a gift when you already owned a game in a bundle.
This is not true. Valve definitely still gives you extra copies of games if you buy one of their game packs. (Orange Box, Half Life Collection, etc).
However, this is *only* for Valve games. Most game bundles from other publishers (with a few exceptions) will not give you extra copies of games to give away, so the extra game you just paid for disintegrates. This is not Valve's fault. This is the decision of the publisher.
There's a lot of legal mumbo-jumbo between Valve and PC games publishers when they agree to sell their games on Steam; and usually the distribution agreement doesn't allow for extra giftable copies. It's unfortunate, yes; but that's just kind of the way it is. Valve has no control over it. Blame the publisher, not Valve.
I remember that too, HL2 was giftable if you already owned it and then say bought the Orange Box.
So it's obviously technically feasible. How hard is it to have each game have a key?
I'm just saying, I should have a gift able copy when I buy more than one no matter how it's sold or packaged.
If I buy two Chevy Volts I get 2 copies to do anything I want with. If I buy two identical dishes I can do whatever with either one. To me Valve (and other distro sites) are really taking advantage of the consumer by not giving them access to the 2 copies they paid for.
If you look at most other bundle sites out there that give away Steam keys (such as Indie Royale, Indie Gala, Groupees, etc, etc), you'll see that just about all of them give separate keys for each game. In fact, Humble Bundle is the *only* store that groups all the games into one key.
As for why they decide to do this, I'm not sure. I'm sure a big part of it is to prevent abuse and keep people from hoarding keys and selling them off separately for profit. THQ may have also had a say in it as well.
But in general, if you have a complaint about the way Humble Bundle distributes keys; take it up with the Humble store. Don't blame it on Valve. Valve has almost nothing to do with it.