Is the MRI C extension API compatibility an official 
     feature now?

Yes, because there's lots of code out there that's targeting that API and you don't want to throw good, stable and tested code away.

    without having to worry about finding alternatives 
    for all the libs I'm using that carry C-extension 
    baggage

It's not really baggage that you don't want. It's only baggage in the sense that backwards-compatibility makes forward progress harder, but if you can come up with a way to maintain compatibility with an emulation layer of some sort, than that's the best of both worlds.

    EngineYard really should clarify their vision behind 
    maintaining two VMs

It's not EngineYard's business to clarify their vision behind these 2 VMs, as both projects were started outside of EngineYard. This company is doing the Ruby community a favor by paying developers for working on these 2 projects, but the projects themselves would go on without EngineYard.