Bunny Must Die is a perfect example of how a non-steamworks title can still hand out keys. You'd think that if it costs so much to hand out keys for Square Enix, indie companies wouldn't do it.
Square Enix also mentions how the game must be completely downloaded all over again, I really doubt this since this game uses a launcher to update the main game. More so, I could see Square being able to roll out keys should they decide to do it. Bunny Must Die is NOT the only indie company that isn't steamworks and still handed out steam keys.

Indie Royale and Humble Bundles give away steam keys once any game sold ends up on steam. I see Square Enix shouldn't have as much trouble as they're mentioning, least have an official statement as to why this isn't happening.