It's using Cocoa on OS X and WPF on Windows, in other words the UI toolkits that are native to their respective platforms. Qt indeed works everywhere, but by using it you make the tradeoff that your app doesn't really feel native anywhere (except maybe on Linux with KDE).
In short, using Qt would mean making concessions on UI quality.
I find it hard to look at their windows UI and think "native".
I'm wrong, as it was explicitly designed in windows 8's "Metro" style in mind [https://github.com/blog/1151-designing-github-for-windows]. Nevertheless, the concept of a "native" windows style is currently such a mixed mess that I can't bring myself to think of this app as "native". I don't see why being native to Metro is desirable enough to give up the convenience of having a single cross-platform app.
[I'm not saying I don't like the design, I do. It's just that I care about its features — simplicity and github integration — as something I can recommend to git newbies — much more that "nativeness".]
I don't think non-cocoa or non-WPF necessarily means worse quality, you just have to do a bit more custom work. Take Slack (using the Electron framework), or Telegram's Qt client.
Having said that, Qt Quick Controls could definitely be improved by having better default desktop QML UI widgets.
I use Slack on a daily basis and I can't say I'm happy with it being an Electron app. For what it does it's very resource intensive and the way it disregards a lot of its host OS conventions isn't cool. If I wanted a web app I'd open another browser tab; there's no need for a goofy wrapper with half-hearted OS integration.
I also use it daily, and agree with what you are saying about it being a resource hog. That said, I find it pretty good for the most part, and being cross-platform for free is killer.
I'm on OSX and Linux, most of my team are on Linux, I'm not sure they would have taken the trouble to release a Linux version without Electron.
I think the problem is that in user interfaces pretty good can be a million miles from good. It's like the uncanny valley in animation - the app feels wrong or ill but I can't quite tell why and it's very off-putting.
