We see a future where these two projects _probably_ merge, but not just yet. I think the mobile-first, one-web community has a little more work to tackle. For now the mobile boilerplate is ideal for mobile-only webapps (like with PhoneGap).
I find it rather straightforward to modify H5BP into a responsive design, anyway. When the time comes for mobile-only to die, it's not going to be a difficult transition. No rush.
I wonder if they're implying we should use html5 v2 for mobile now. I know v2 has a "mobile-first" focus...