Basically, the WHATWG and W3C specs have diverged and there is no clear plan for them to meet up again. So, just because WHATWTG has added bitcoin links to their HTML5 spec does not mean that W3C will add bitcoin links to theirs. W3C is generally considered the more respected/"official" spec out of the two. (I would not be surprised if most people who've heard of the W3C have not heard of WHATWG.) I know that browser developers care about being W3C-compliant. I'm not sure whether they care about being WHATWG-compliant.
Browser developers care about being “WhatWG compliant”, because the WhatWG HTML group is composed by browser editors, they work with the W3C HTML5 group, and the HTML5 specification is based on the WhatWG’s HTML document.
WhatWG HTML is the living standard, and the HTML5 (W3C) spec. is like a snapshot.
http://wiki.whatwg.org/wiki/FAQ#What_is_HTML5.3F