The article is pretty clear about your question. This is just going to provide cross platform messaging between all current and future apps.
Most likely though in the background they will use these links as ways to package your identity up when selling to advertisers. Thats what I'm guessing is the end goal , enrich their stagnant platform (FB) with their growth platforms (WhatsApp and Instagram)
While it would be great if they moved to a pure Jabber federation model or similar, I very much doubt they will do that, however, unless someone like the EU can get their act together and force them to do it.