Flipboard addresses the accessibility issue in their article. While moving to canvas limits it for now, at least they are making an effort to incorporate it, which is more than can be said for most sites.
It's a world of trade-offs. There are contexts where accessibility is obvious more important than most other concerns -- the IRS's web site should obviously be as accessible as possible because everybody needs to pay their taxes. On the flip side of things, the point of Flipboard IS the UI. Flipboard is all about aggregating other people's content and providing a different user interface to it. What Flipboard is doing is it is taking limited resources and trying to allocate them, and they're choosing to focus on improving the user experience for the vast majority of their users. Is that the right choice? I dunno. But I don't think condescendingly referring to their focus on user experience as "whooshy effects" adds anything to the conversation.