Last time I checked, Qt still used completely its own rendering, input handling, etc, imitating platform. So it's conceptually not different from, e.g. Java Swing. Probably imitation is better.
That said, Windows is bad at UX consistency. Native used to mean WinAPI with built-in window classes handling input, buttons, etc (and wrappers like MFC or Windows Forms). Then it was WPF with its own DirectX-based stack. Now it's UWP with even different code. I guess, Qt is not the worst solution. macOS is much more coherent ecosystem when it comes to native.
So it's true that Qt may not be perfect at mimicking native Windows UI, but in practice people don't seem to care too much for apps if the end result is still ergonomic & responsive and integrates nicely with the overall OS (unlike Swing or XUL). And Qt seems to do that quite well. In practice, I'm not sure anyone would even want a mIRC-style pure-windows UI Matrix client...
