Not exactly an "independent" publisher, only available for Steam, only for Windows, no contributions to the EFF? But when you add in that there is no DRM-free version, it's just not "Humble Bundle" anymore.
They dropped the EFF because that's what the developers voted on it would seem https://twitter.com/humble/status/146655575290286080
But if it were me in charge, I'd list 3 charities. One would be the charity that, last time, had received the greatest portion of the contributions from people who had adjusted the contribution sliders rather than accepting the default value. One would be a new charity never before featured on Humble Bundle. The last would flex, depending on circumstances: it could be a charity favored by the Humble Bundle team, one chosen by the app developers, or perhaps the second-favorite from contributors who adjusted sliders.