I feel like it's a spectrum. The simpler the app, the more likely it's better to try an integrate with a closer to native look. I always found the issue of "native" to be a bit funny to me as someone coming from the 3D/VFX space, since all of the applications are built to be multiplatform and don't give a hoot about "native". Consistency of the application experience across platforms trumps all. The number of people I've seen complain about this? Zero. Usually the only issues arise around file pickers (some have custom ones, others use platform ones which have differences).

Granted these applications boast a ridiculous amount of features and are incredibly complex putting them on the opposite end of the spectrum compared to simple GUIs and chat/productivity applications.

To me, it's nice that platforms provide native toolkits* to provide this level of integration. But I don't view any app as "native" unless it comes from the party making the platform, as they are really the only ones that actually have to adhere to their human interface guidelines to the fullest extent.

* On Linux this is more up-in-the-air. I personally don't consider GTK and Qt as native toolkits, but the foundational pairing for things like libadwaita and KDE Frameworks which provide the associated platform widgets and HIG. Using the toolkits directly is fine and will mostly work, but it's not the same as a "native" application.