A quarter-century ago, yes. If they haven't migrated to native widgets in 25 years, that might be an indicator of something
But the premise is silly: if Linux has two native toolkits, how is this a sensible recommendation?? Hint: it isn’t, because GTK/Qt are not the native, but rather simply the most used.
Also, go to Mac, and SwiftUI still doesn’t support all that AppKit used to, leaving an incentive for developers to deviate from the platform’s recommendation.
And back to Windows, WinUI still doesn’t fully replace Win32 or Windows Forms, so same conclusion applies.
I’m going to hazard the claim that in probably most people’s conception of the term, GTK is native in GNOME, Cinnamon, Xfce, etc. and Qt is native in KDE, LXQt and Sailfish OS.