Is Qt considered native when you use KDE and not native when you use GNOME? Is Qt 3 considered not native when you use a KDE release that uses Qt 4 under the hood?
A similar thing happened to Android.
Windows 10 has several native GUI toolkits. The same thing happened in MacOS, which transitioned from Carbon to Cocoa.
If the widgets are drawn by a toolkit that isn't bundled with the OS, it's a non-native GUI. Of course, this isn't always a bad move.