While I would love more competition in this space, I doubt if MS will offer a native app. They have recently moved Skype to an electron app (basically the website in a wrapper)[0] so I don't expect this to be any different. While this is in alpha (and only for linux), I expect them to move all their other clients (apart from Windows) to this electron app.
The Slack desktop app works pretty much the same way - native wrapper around an HTML UI that is almost identical to their web UI. (I think they may use the platform's native webview though, not Electron).
It has its pros & cons... one nice thing is that if you use the desktop app most of the time, using the web UI on the go doesn't feel like much of an adjustment. It has basically the full power of the desktop app because it's the same UI code.
You know, I really should think about my recent experience with a company's product before making comparisons. Because I forgot about the Skype app (don't use Skype much, but their recent releases for Mac were bad), and a few other recent examples that were less than stellar. So I guess a good experience with the Microsoft product isn't a given lately (I'm looking at you, Lync for Mac).
[0] http://www.omgubuntu.co.uk/2016/07/skype-linux-alpha