If you care about your privacy...
..then you have already stopped obsessing with "apps" and are primarily concerned with protocols. Once you have decided on, say, XMPP plus OpenPGP extensions, then you have plenty of competing apps to chose from.
And of course, it follows that whatever protocol you use, will be "service-agnostic." Since you're going to pick something which uses a secure protocol, you basically don't care about servers; they're all commodities. Install jabberd or whatever at your Linode. Seriously: whatever.
I don't know how WhatsApp or Allo are even seriously considered. What do they speak? When people talk about the app more than the protocol, that's a bad sign. (e.g. I use the web and it's irrelevant whether I use it with Chromium or Firefox. The more you care about my specific browser, the more I think you're trying to talk me into not-using-the-web.)
This gets modded as Insightful? Really?
Hence the fricking article.