Apollo is flexible in a lot of really significant ways, many of which will become clear after we launch a new API we're working on. Basically the idea is that it integrates with your existing workflow, and is easy to contribute to and extend.
The discussion you linked to does not say that Relay will support subscriptions, but rather that it will be possible to implement subscriptions in user space, meaning as an external package. Apollo has this support built-in, and it will integrate nicely with all of the different parts.
Besides, we already have all of the features that "should be possible with this new API" in Relay.
Either way, given how long Apollo and Relay have been around, I'd say it's a pretty great achievement that we have about equivalence in features, and I expect that Apollo will gain cutting-edge features much faster starting from this point, especially because it's more flexible and community-oriented.
As an example of what it means for something to be supported out of the box, consider how easy it is to do SSR with Apollo today: http://dev.apollodata.com/react/server-side-rendering.html