I'm not sure if what I'm thinking is correct (or even technically possible) - but couldnt it be possible that what they are envisioning is the Rubinius architecture being the one true Ruby and having two backends : C-Rubinius or Java-Rubinius.

What it would mean is that the C-Rubinius and Java-Rubinius releases be simultaneous: you can choose to pick one or the other based on your surrounding stack.

This would mean that they fund both Jruby and Rubinius till they can be merged.