But it isn't just "buttons looking different", it is also "buttons behaving different". As an example (that i often find annoying in programs with long lists), under Windows Qt scrollbars do not behave like native Windows scrollbars: shift click in Windows should cause the scrollbar to scroll at the point you clicked (like middle click on most X toolkits) but Qt ignores that.

Also it is "buttons not integrating properly". On macOS it is very common for example to have system-wide addons (services i think they are called) that add additional functionality to text fields, like "search with google", "text to speech", "show definition", etc. This doesn't work when a toolkit does its own text field controls. You can also see a similar thing on Windows: GTK+ applications (e.g. GIMP) ignore the emoji panel in their text fields that appear with Windows+; but native text fields work fine with it.

Now note that i'm not saying this is something that matters for all sorts of applications or is always a deal breaker (especially nowadays that, as i wrote above, most users outside of macOS have been conditioned to accept these), but it isn't something that you can handwave away as "having a different shade" either.