You realize that GTK and Qt are both compatible with the other?
Most GTK apps work nicely under Qt (although this is very suboptimal), but especially Qt apps look native everywhere. From windows to mac to KDE-environments to Gtk-environments.
What do you mean by gtk under Qt? What about Tk apps, or Athena apps, or Motif, or GNUStep, etc.? There really is no such thing as a native Linux look and feel, you just happen to use a consistent selection of apps on your own system.
What I mean is that a Qt app will look native everywhere, and Gtk apps will look native in most places.
Most other toolkits, as you mentioned, don’t look native in many places, but Qt natively supports the CDE style, the Motif style, all different Windows and Mac styles, etc.
A Qt app looks native on Mac OSX, on Solaris, under Gnome, under KDE, under Windows XP, under Windows 10.
That’s why I avoid apps that aren’t either native or Qt anywhere, no matter if I am running Gnome or Windows, KDE or Mac.
By asking for a "Linux native application", you would need to create forks for GTK/Qt theming at the minimum and change the appearance altogether. It's just an absurd request really. One thing Electron does not do well is per-system graphical elements. It renders the same on every system so you either have a unique application design or you're conforming more to Window, Mac, or GNU/Linux. Or doom yourself to an old stale design, which is bland enough to fit in every category, but isn't the aim of the project.