I really hope we can see a unification of the efforts and work through the political issues. Having very talented developers working on separate codebases instead of improving one seems counterproductive.
As it was already said they run the same package manager and claim compatibility. This means you either can't take advantage of any new API in io.js ever to allow your module to work in both or you take the road where you're transpiling to support one and the other. It's not sustainable and it's prone to issues.